A manuscript was published at Bioinformatics (https://academic.oup.com/bioinformatics/article/36/18/4813/5906504).
ver3.0.1: Supported to netMHCpan4.1 and netMHCIIpan4.3.
Install R from the official (https://www.r-project.org/).
or
CentOS
[command line]
yum -y install R
Mac(Devian)
[command line]
brew cask install r
Anaconda
[command line]
conda -n create Neoantimon r-essentials r-base
conda activate Neoantimon
conda update --all
Notice: If you're using M1/M2/M3 MacOS, you need to install available version conda.
This code is a simple sample code for preliminary use to confirm the output.
[R]
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
install.packages("devtools");
library(devtools);
BiocManager::install("ensemblVEP")
install_github('hase62/Neoantimon');
library(Neoantimon);
data("sample_vcf.annovar")
data("sample_hla_table_c1")
data("sample_refFlat.grch37")
data("sample_refMrna.grch37.fa")
data("sample_result_SNV_CLASS1_ALL")
MainSNVClass1(input_annovar_format_file = sample_vcf.annovar,
hla_types = sample_hla_table_c1[1,-1],
refflat_file = sample_refFlat.grch37,
refmrna_file = sample_refMrna.grch37.fa,
netMHCpan_dir = NA)
write.table(file = "result.ID.SNV1/data.ID_SNV.peptide.SNV_CLASS1_ALL.txt",
x = sample_result_SNV_CLASS1_ALL[grep("0_DHX15", sample_result_SNV_CLASS1_ALL$Gene), ],
row.names = FALSE, quote = FALSE, sep = "\t")
You can get the following outputs.
data.ID_SNV.peptide.txt (annotation file)
## Number GeneSymbol NM_id AAchanges Ref Alt Prob Mutation_Prob Exon_Start Exon_End Mutation_Position Evaluated_Mutant_Peptide Evaluated_Wt_Peptide ..
## 1 0_DHX15 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD ..
data.ID_SNV.peptide.fasta (input file for netMHCpan)
## >0_DHX15
## PEPERDYLEAAIRAVIQIHMCEEEEGD
data.ID_SNV.wtpeptide.fasta (input file for netMHCpan)
## >0_DHX15
## PEPERDYLEAAIRTVIQIHMCEEEEGD
data.ID_SNV.peptide.SNV_CLASS1_ALL.txt (output file)
## HLA Pos Gene Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Evaluated_Wt_Peptide Wt_IC50 Wt_Rank Chr NM_ID Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## HLA-A*02:01 2 0_DHX15 EPERDYLEAAIRA 37952.9 63.3899 EPERDYLEAAIRT 41213.3 75.7538 4 NM_001358 c.A1012G T C 0 0 24529087 24586184 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624897959184 NA NA NA
## HLA-A*02:01 3 0_DHX15 PERDYLEAAIRAV 12108.2 16.51 PERDYLEAAIRTV 11859.7 16.2523 4 NM_001358 c.A1012G T C 0 0 24529087 24586184 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624897959184 NA NA NA
## HLA-A*02:01 4 0_DHX15 ERDYLEAAIRAVI 12109.5 16.5114 ERDYLEAAIRTVI 14831.9 19.2905 4 NM_001358 c.A1012G T C 0 0 24529087 24586184 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624897959184 NA NA NA
## ..
##
CentOS
[command line]
yum install wget
Mac(Devian)
[command line]
brew install wget
Anaconda
[command line]
conda install -c anaconda wget
-
Download netMHCpan4.1 from https://services.healthtech.dtu.dk/services/NetMHCpan-4.1 and move it to any working directory. (Assume you have netMHCpan-4.1b.{Darwin|Linux}.tar.gz in your "lib" directory.)
-
Run the initial setting script at the directory that contains downloaded as followings.
We have
lib/
└ netMHCpan-4.1b.{Darwin|Linux}.tar
Run
[command line]
wget --no-check-certificate https://github.com/hase62/Neoantimon/raw/master/lib/setNetMHCpan4.1.sh
chmod 750 setNetMHCpan4.1.sh
./setNetMHCpan4.1.sh
Notice: If you're using M1/M2 MacOS, you should additionally replace lib/netNetMHCpan-4.1/netMHCpan as follows
set PLATFORM = echo $UNIX $AR | awk '{print $1"_"$2}'
to
set PLATFORM = echo $UNIX x86_64 | awk '{print $1"_"$2}'
We have
lib/
├ netMHCpan-4.1b.{Darwin|Linux}.tar
├ setNetMHCpan4.1.sh
└ NetMHCpan4.1/
├ {Darwin|Linux}_x86_64
├ data
├ data.{Darwin|Linux}.tar.gz
├ netMHCpan
├ netMHCpan-4.1.readme
├ netMHCpan-e
├ netMHCpan.1
├ test
└ tmp
- (Recommended) Install anaconda from https://www.anaconda.com/distribution/, and then run the following codes.
[command line]
pip install mhcflurry
pip install tensorflow
mhcflurry-downloads fetch
or
[command line]
pip install mhcflurry
conda install -c conda-forge tensorflow
mhcflurry-downloads fetch
Notice: If you're using M1/M2 MacOS, you should install M1/M2 available version tensorflow.
- Otherwise, install python from https://www.python.org/downloads/release, and then run the above codes.
-
Download netMHCIIpan 4.2 from https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.2 and move it to the working directory. (Assume you have netMHCIIpan-4.2.{Darwin|Linux}.tar.gz in your "lib" directory.)
-
Do initial setting at the working directory as followings.
We have
lib/
└ netMHCIIpan-4.2.{Darwin|Linux}.tar
Run
[command line]
wget --no-check-certificate https://github.com/hase62/Neoantimon/raw/master/lib/setNetMHCIIpan4.2.sh
chmod 750 setNetMHCIIpan4.2.sh
./setNetMHCIIpan4.2.sh
Notice: If you're using M1/M2 MacOS, you should additionally replace lib/netNetMHCpan-4.2/netMHCpan as follows
set PLATFORM = echo $UNIX $AR | awk '{print $1"_"$2}'
to
set PLATFORM = echo $UNIX x86_64 | awk '{print $1"_"$2}'
We have
lib/
├ netMHCIIpan-4.2.{Darwin|Linux}.tar
├ setNetMHCIIpan4.2.sh
└ netMHCIIpan-4.2/
├ {Darwin|Linux}_x86_64
├ data
├ netMHCIIpan
├ NetMHCIIpan-4.2.pl
├ netMHCIIpan-4.2.readme
├ netMHCIIpan-e
├ etMHCIIpan.1
├ test
├ test.fa
└ tmp
(You have to select your corresponding version from GRCh38, hg38, GRCh37 or hg19.)
GRCh38/hg38: Run the following codes.
[command line]
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/refMrna.fa.gz
gunzip refMrna.fa.gz
mv refMrna.fa refMrna.grch38.fa
GRCh37/hg19: Run the following codes.
[command line]
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/refMrna.fa.gz
gunzip refMrna.fa.gz
mv refMrna.fa refMrna.grch37.fa
(You have to select your corresponding version from GRCh38, hg38, GRCh37 or hg19.)
GRCh38/hg38: Run the following codes.
[command line]
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz
gunzip refFlat.txt.gz
mv refFlat.txt refFlat.grch38.txt
GRCh37/hg19: Run the following codes.
[command line]
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
gunzip refFlat.txt.gz
mv refFlat.txt refFlat.grch37.txt
- (Recommended) Install anaconda from https://www.anaconda.com/distribution/, and then run the following codes.
[command line]
conda install -c bioconda samtools
- Otherwise, you can install local samtools as followings.
[command line]
wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2
tar jxf samtools-0.1.19.tar.bz2
(You have to select your corresponding version from GRCh38, hg38, GRCh37 or hg19.)
GRCh38: Run the following codes.
[command line]
wget ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
mv Homo_sapiens.GRCh38.dna.toplevel.fa.gz GRCh38.fa.gz
gunzip GRCh38.fa.gz
samtools faidx GRCh38.fa
hg38: Run the following codes.
[command line]
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz
samtools faidx hg38.fa
GRCh37/hg19: Run the following codes.
[command line]
wget ftp://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.toplevel.fa.gz
mv Homo_sapiens.GRCh37.75.dna.toplevel.fa.gz GRCh37.fa.gz
gunzip GRCh37.fa.gz
samtools faidx GRCh37.fa
Required
[R]
install.packages("devtools");
library(devtools);
install_github('hase62/Neoantimon');
library(Neoantimon);
If you're using Anaconda,
[command line]
conda install -c conda-forge r_devtools
Then,
[R]
library(devtools);
install_github('hase62/Neoantimon');
library(Neoantimon);
Suggested to Install for Reading Data at High Speed
[R]
install.packages('data.table');
library(data.table);
1. A HLA Class I table file must be according to the following format.
[R]
data("sample_hla_table_c1")
print(sample_hla_table_c1, row.names = FALSE)## Name A1 A2 B1 B2 C1 C2
## sample A*02:01 A*32:01 B*15:17 B*51:01 C*07:01 C*15:02
## sample2 A*02:01 A*32:01 B*15:17 B*51:01 C*07:01 C*15:02
2. A HLA Class II table file must be according to the following format.
[R]
data("sample_hla_table_c2")
print(sample_hla_table_c2, row.names = FALSE)## Name DPA11 DPA12 DPB11 DPB12 DQA11 DQA12 DQB11 DQB12 DRB11 DRB12
## sample DPA1*01:03 DPA1*02:01 DPB1*02:01 DPB1*09:01 DQA1*01:02 DQA1*05:05 DQB1*03:01 DQB1*06:04 DRB1*11:04 DRB1*13:02
## sample2 DPA1*01:03 DPA1*02:01 DPB1*02:01 DPB1*09:01 DQA1*01:02 DQA1*05:05 DQB1*03:01 DQB1*06:04 DRB1*11:04 DRB1*13:02
An annovar format or an Ensembl Variant Effect Predictor (VEP) format annotated vcf file is required for Snv/Indel.
When indicating annovar format, it must include columns representing "Chromosome Number", "Mutation Start Position", "Mutation End Position", "Mutation Ref", "Mutation Alt", and "NM_ID (AAChange.refGene)". Annotations "Chr", "Start", "End", "Ref", "Alt", "AAChange.refGene", "Depth_tumor", and "Depth_normal" are automatically detected. Otherwise, you have to manually indicate columns.
[R]
data("sample_vcf.annovar")
print(sample_vcf.annovar, row.names = FALSE)## Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene cytoBand depth_tumor variantNum_tumor depth_normal
## 1 116941338 116941338 T C exonic ATP1A1 synonymous SNV ATP1A1:NM_001160234:exon16:c.T2127C:p.D709D 1p13.1 100 39 111
## 4 24556416 24556416 T C exonic DHX15 nonsynonymous SNV DHX15:NM_001358:exon5:c.A1012G:p.T338A 4p15.2 143 47 151
## 4 70156404 70156404 - T exonic UGT2B28 frameshift insertion UGT2B28:NM_053039:exon5:c.1186dupT:p.L395fs 4q13.2 43 15 41
## 6 75899298 75899298 T - exonic COL12A1 frameshift deletion COL12A1:NM_004370:exon6:c.628delA:p.I210fs 6q13 122 38 73
## 9 89561162 89561162 C T exonic GAS1 nonsynonymous SNV GAS1:NM_002048:exon1:c.G533A:p.R178H 9q21.33 20 5 26
...
[R]
data("sample_vcf.vep")
print(sample_vcf.vep, row.names = FALSE)## Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra
## file_name 1:1290161 A ENSG00000162576 ENST00000309212 Transcript missense_variant 881 850 284 R/C Cgc/Tgc - IMPACT=MODERATE;STRAND=-1
## file_name 1:1434364 T ENSG00000160072 ENST00000474481 Transcript downstream_gene_variant - - - - - - IMPACT=MODIFIER;DISTANCE=2783;STRAND=1
## file_name 1:12919618 A ENSG00000120952 ENST00000240189 Transcript missense_variant 445 358 120 W/R Tgg/Agg - IMPACT=MODERATE;STRAND=1
## file_name 1:16890602 G ENSG00000219481 ENST00000430580 Transcript missense_variant 4144 3256 1086 M/L Atg/Ctg - IMPACT=MODERATE;STRAND=-1
## file_name 1:16918457 C ENSG00000219481 ENST00000392963 Transcript "missense_variant,NMD_transcript_variant" 518 60 20 I/M atC/atG - IMPACT=MODERATE;STRAND=-1
## file_name 1:20297876 G ENSG00000188257 ENST00000482011 Transcript downstream_gene_variant - - - - - - IMPACT=MODIFIER;DISTANCE=4290;STRAND=-1
## file_name 1:48906934 T ENSG00000132122 ENST00000487543 Transcript "intron_variant,NMD_transcript_variant" - - - - - - IMPACT=MODIFIER;STRAND=-1
...
Please install the following library when you use vep-annotated files.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")
library(biomaRt)
For example, please run as following.
MainSNVClass1(input_vep_format_file = sample_vcf.vep,
hla_types = sample_hla_table_c1[1,-1],
refflat_file = sample_refFlat.grch37,
refmrna_file = sample_refMrna.grch37.fa,
netMHCpan_dir = NA)
An annotated BND format vcf file is required for SV fusion.
It must include columns representing "Chromosome Number", "Mutation Start Position", "Mutation End Position", "Mutation Ref", "Mutation Alt", and "NM_ID (AAChange.refGene)" or "Gene Symbol (Gene.refGene)". Annotations "Chr", "Start", "End", "Ref", "Alt", "Depth_tumor", and "Depth_normal" are automatically detected. Otherwise, you have to manually indicate columns.
[R]
data("sample_sv_bnd")
print(sample_sv_bnd, row.names = FALSE)## Chr Start End Ref Alt Func.refGene Gene.refGene mateID
## 1 115005805 115005805 C C]20:34827929] exonic TRIM33 SVMERGE137_1
## 1 204908711 204908711 A [2:172743385[A intronic NFASC SVMERGE15_1
## 2 25870534 25870534 T ]2:25965720]G intronic DTNB SVMERGE116_1
## 2 25965720 25965720 T T[2:25870536[ exonic ASXL2 SVMERGE116_2
## 2 214794791 214794791 C C[2:214798169[ exonic SPAG16 SVMERGE3_1
## 2 214798169 214798169 T ]2:214794791]T intronic SPAG16 SVMERGE3_2
...
An RNA expressoin file is not required, but you can attach "RNA expression" information by indicating "rnaexp_file". If you also indicate "rnabam_file", variant allele frequencies and tumor specific RNA expressions are also attached to the results.
[R]
data("sample_rna_exp")
print(sample_rna_exp, row.names = FALSE)## gene_short_name ChromosomeNum:Start-Endlocus expression
## 7SK HSCHR6_MHC_MCF:30910595-30910898 0.00000000
## 7SK HSCHR6_MHC_QBL:30821624-30821927 0.00000000
## 7SK X:12632121-12632316 0.00000000
## A1BG 19:58856543-58864865 0.19541613
## A1BG-AS1 19:58859116-58866549 5.30484229
## A1CF 10:52559168-52645435 4.78487242
## A2M 12:9220259-9268825 0.75619084
## A2M-AS1 12:9217772-9220651 4.15985770
## A2ML1 12:8975067-9039597 7.50201326
## A2ML1-AS1 12:8928814-8983543 0.00000000
## A2ML1-AS2 12:8972411-8973309 7.02685468
## A2MP1 12:9381128-9428413 4.36764217
## A3GALT2 1:33772366-33786699 0.00000000
## A4GALT 22:43088126-43117304 2.27225123
## A4GNT 3:137842559-137851229 0.00000000
## AAAS 12:53701239-53718648 1.45197987
## AACS 12:125549924-125627873 7.34085879
## AACSP1 5:178191861-178245436 4.07342571
## AADAC 3:151531824-151546276 0.61589770
## AADACL2 3:151451703-151479127 0.01359431
## AADACL2 HSCHR3_1_CTG2_1:151462241-151489665 0.00000000
A copynumber file is not required, but you can attach "Copy Number" information by indicating "cnv_file" and "purity" in main functions. They are used to calculate tumor subclonal cell population. Purity is set 1 as default value.
[R]
data("sample_copynum")
print(sample_copynum, row.names = FALSE)## Chromosome Position Log.R segmented.LogR BAF segmented.BAF Copy.number Minor.allele Raw.copy.number
## 1 564621 0.6071447 -0.09862298 1 NA 2 1 4.3540752
## 1 799463 0.1519967 -0.09862298 1 NA 2 1 2.1467339
## 1 1017216 0.8146911 -0.09862298 0 NA 3 1 5.8658499
## 1 1158277 -1.9594627 -0.09862298 0 NA 1 0 -0.5035897
## 1 1242215 0.2927962 -0.09862298 0 NA 2 1 2.6999875
## 1 1462766 -0.2234090 -0.09862298 1 NA 2 1 1.0726687
Run the following codes. (We assume that data will be downloaded into "lib" directory)
[command line]
wget --no-check-certificate https://github.com/hase62/Neoantimon/raw/master/lib/data.zip
unzip data.zip
We assume the following directory structure according to 1. Preparation.
~/opt/anaconda3
lib/
├ NetMHCpan4.0
├ netMHCIIpan-3.2
├ refFlat.grch37.txt
├ refMrna.grch37.fa
└ data/
├ sample_result_INDEL_CLASS1_ALL.txt
├ sample_result_INDEL_CLASS2_ALL.txt
├ sample_result_SeqFragment_CLASS1_ALL.txt
├ sample_result_SeqFragment_CLASS2_ALL.txt
├ sample_result_SNV_CLASS1_ALL.txt
├ sample_result_SNV_CLASS2_ALL.txt
├ sample_result_SVFusion_CLASS1_ALL.txt
├ sample_result_SVFusion_CLASS2_ALL.txt
├ sample_copynum.txt
├ sample_hla_table_c1.txt
├ sample_hla_table_c2.txt
├ sample_refMrna.grch37.fa.txt
├ sample_refFlat.grch37.txt
├ sample_rna_exp.txt
├ sample_vcf.annovar.txt
├ sample_vcf.vep.txt
├ sample_sv_bnd.txt
└ sample_vcf.snps.vcf
To calculate the binding affinity of neoantigen candaites, which are generated from from SNVs, to HLA ClassI. When using MHCflurry, [[1]] and [[2]] include the results of NetMHCpan and MHCflurry, respectively.
[R]
Result_HLA1_SNV <- MainSNVClass1(input_annovar_format_file = "data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c1.txt",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
rnaexp_file = "data/sample_rna_exp.txt",
netMHCpan_dir = "netMHCpan-4.0/netMHCpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "data/sample_vcf.snps.vcf",
multiple_variants = TRUE,
MHCflurry = "~/opt/anaconda3/bin/mhctools")
Result_HLA1_SNV_1 <- CalculatePriorityScores(result = Result_HLA1_SNV[[1]], useRNAvaf = FALSE)
Result_HLA1_SNV_2 <- CalculatePriorityScores(result = Result_HLA1_SNV[[2]], useRNAvaf = FALSE)
[R]
Result_HLA1_SNV_vep <- MainSNVClass1(input_vep_format_file = "data/sample_vcf.vep.txt",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c1.txt",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
rnaexp_file = "data/sample_rna_exp.txt",
netMHCpan_dir = "netMHCpan-4.0/netMHCpan",
multiple_variants = FALSE)
Result_HLA1_vep_SNV <- CalculatePriorityScores(result = Result_HLA1_SNV_vep, useRNAvaf = FALSE)
To calculate the binding affinity of neoantigen candaites, which are generated from from SNVs, to HLA ClassII.
[R]
Result_HLA2_SNV <- MainSNVClass2(input_annovar_format_file = "data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c2.txt",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
rnaexp_file = "data/sample_rna_exp.txt",
netMHCIIpan_dir = "netMHCIIpan-3.2/netMHCIIpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "data/sample_vcf.snps.vcf",
multiple_variants = TRUE)
Result_HLA2_SNV <- CalculatePriorityScores(result = Result_HLA2_SNV, useRNAvaf = FALSE)
To calculate the binding affinity of neoantigen candaites, which are generated from from indels, to HLA ClassI. When using MHCflurry, [[1]] and [[2]] include the results of NetMHCpan and MHCflurry, respectively.
[R]
Result_HLA1_INDEL <- MainINDELClass1(input_annovar_format_file = "data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c1.txt",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
rnaexp_file = "data/sample_rna_exp.txt",
netMHCpan_dir = "netMHCpan-4.0/netMHCpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "data/sample_vcf.snps.vcf",
multiple_variants = TRUE,
MHCflurry = "~/opt/anaconda3/bin/mhctools")
Result_HLA1_INDEL_1 <- CalculatePriorityScores(result = Result_HLA1_INDEL[[1]], useRNAvaf = FALSE)
Result_HLA1_INDEL_2 <- CalculatePriorityScores(result = Result_HLA1_INDEL[[2]], useRNAvaf = FALSE)
To calculate the binding affinity of neoantigen candaites, which are generated from from indels, to HLA ClassII.
[R]
Result_HLA2_INDEL <- MainINDELClass2(input_annovar_format_file = "data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c2.txt",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
rnaexp_file = "data/sample_rna_exp.txt",
netMHCIIpan_dir = "netMHCIIpan-3.2/netMHCIIpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "data/sample_vcf.snps.vcf",
multiple_variants = TRUE)
Result_HLA2_INDEL <- CalculatePriorityScores(result = Result_HLA2_INDEL, useRNAvaf = FALSE)
To calculate the binding affinity of neoantigen candaites, which are generated from from SVs, to HLA ClassI.
[R]
Result_HLA1_SV <- MainSVFUSIONClass1(input_file = "data/sample_sv_bnd.txt",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c1.txt",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
rnaexp_file = "data/sample_rna_exp.txt",
netMHCpan_dir = "netMHCpan-4.0/netMHCpan",
mutation_alt_bnd_column = 5,
gene_symbol_column = 7,
mate_id_column = 8)
Result_HLA1_SV <- CalculatePriorityScores(result = Result_HLA1_SV, useRNAvaf = FALSE)
To calculate the binding affinity of neoantigen candaites, which are generated from from SVs, to HLA ClassII.
[R]
Result_HLA2_SV <- MainSVFUSIONClass2(input_file = "data/sample_sv_bnd.txt",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c2.txt",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
rnaexp_file = "data/sample_rna_exp.txt",
netMHCIIpan_dir = "netMHCIIpan-3.2/netMHCIIpan",
mutation_alt_bnd_column = 5,
gene_symbol_column = 7,
mate_id_column = 8)
Result_HLA2_SV <- CalculatePriorityScores(result = Result_HLA2_SV, useRNAvaf = FALSE)
Calculate Neoantigens from a fragment of RNA sequence for HLA Class I and II by comparing to the original protein.
To calculate the binding affinity of neoantigen candaites, which are directly generated from RNA sequences, to HLA ClassI. The peptides included in the original genes ("NM_003998", "NM_001165412") are removed from the results.
[R]
Result_HLA1_Seq <- MainSeqFragmentClass1(input_sequence = "atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c1.txt",
hmdir = getwd(),
job_id = "NO_job_id",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
netMHCpan_dir = "netMHCpan-4.0/netMHCpan",
reference_nm_id = c("NM_003998", "NM_001165412"))
To calculate the binding affinity of neoantigen candaites, which are directly generated from RNA sequences, to HLA ClassII. The peptides included in the riginal genes ("NFKB1", "BCL3") are removed from the results.
[R]
Result_HLA2_Seq <- MainSeqFragmentClass2(input_sequence = "atggcagaagatgatccatatttgggaaggcctgaacaaatgtttcatttgatccttctttgactcatacaatatttaatc",
file_name_in_hla_table = "sample",
hla_file = "data/sample_hla_table_c2.txt",
hmdir = getwd(),
job_id = "NO_job_id",
refflat_file = "refFlat.grch37.txt",
refmrna_file = "refMrna.grch37.fa",
netMHCIIpan_dir = "netMHCIIpan-3.2/netMHCIIpan",
reference_gene_symbol = c("NFKB1", "BCL3"))
Users can optionally provide (a) RNA expression data with and without (b) the corresponding Binary Alignment Map (BAM) file to attach total and allele specific RNA expression levels, and (c) copy number variation data to calculate the posterior probability distribution over cancer-cell fraction (CCFP) to evaluate tumor sub-clonality (Lohr et al., 2014).
In addition, users can consider specific cases of existing SNPs on the mutant peptide by providing (c) SNPs data, and multiple SNVs on the same mutant peptides and among the frameshift region caused by indels. These cases are explained as followings.
Results generated from SNVs.
[R]
print(head(Result_HLA1_SNV_1))
## HLA Pos Gene Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Evaluated_Wt_Peptide Wt_IC50 Wt_Rank Chr NM_ID Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## HLA-A*02:01 2 0_DHX15 EPERDYLEAAIRA 37952.9 63.3899 EPERDYLEAAIRT 41213.3 75.7538 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624898 NA NA NA 5.91658748974738e-245 2.81458414604976e-134 2.10034820258638e-134
## HLA-A*02:01 3 0_DHX15 PERDYLEAAIRAV 12108.2 16.51 PERDYLEAAIRTV 11859.7 16.2523 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624898 NA NA NA 1.36530675067013e-76 1.76939032379777e-32 1.32038539031715e-32
## HLA-A*02:01 4 0_DHX15 ERDYLEAAIRAVI 12109.5 16.5114 ERDYLEAAIRTVI 14831.9 19.2905 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624898 NA NA NA 1.33894116890832e-76 1.75704784062078e-32 1.31117496667691e-32
## HLA-A*02:01 5 0_DHX15 RDYLEAAIRAVIQ 32063.2 46.0009 RDYLEAAIRTVIQ 33185.2 48.811 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624898 NA NA NA 1.38049374081809e-206 1.61863141887988e-96 1.20788344383508e-96
## HLA-A*02:01 6 0_DHX15 DYLEAAIRAVIQI 4819.6 9.2763 DYLEAAIRTVIQI 4504.5 8.9225 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD 1.35204 NA NA 0.657624898 NA NA NA 2.48119735063382e-45 2.86275402550381e-22 2.13629437242185e-22
Count the number of neoantigens of which thresholds are IC 50 of mutatnt peptides < 500 and IC 50 of wild-type peptides > 500.
[R]
print(Export_Summary_SNV(Input = Result_HLA1_SNV_1, Mut_IC50_th = 500, Wt_IC50_th = 500))
## Num_All_Alteration Num_Evaluated_Alteration Num_Alteration_Generating_NeoAg Num_All_Peptide Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 3 3 2 189 189 3
Results generated from SNVs.
[R]
print(head(Result_HLA2_SNV))
## HLA Pos Gene Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Evaluated_Wt_Peptide Wt_IC50 Wt_Rank Chr NM_ID Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## HLA-DPA10103-DPB10201 2 0_DHX15 TPEPERDYLEAAIRA 5617.26 75 TPEPERDYLEAAIRT 6356.04 80 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL 1.35204 NA NA 0.657624898 NA NA NA 2.62979323020642e-34 1.73141994214073e-159 1.2920504680954e-159
## HLA-DPA10103-DPB10201 3 0_DHX15 PEPERDYLEAAIRAV 2229.6 55 PEPERDYLEAAIRTV 2571.68 60 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL 1.35204 NA NA 0.657624898 NA NA NA 3.08001102810049e-12 4.65425962615079e-116 3.47318301137882e-116
## HLA-DPA10103-DPB10201 4 0_DHX15 EPERDYLEAAIRAVI 1204.02 39 EPERDYLEAAIRTVI 1404.71 42 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL 1.35204 NA NA 0.657624898 NA NA NA 1.47773566943861e-05 2.578749506743e-81 1.92435955379407e-81
## HLA-DPA10103-DPB10201 5 0_DHX15 PERDYLEAAIRAVIQ 1145.18 38 PERDYLEAAIRTVIQ 1357.96 41 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL 1.35204 NA NA 0.657624898 NA NA NA 3.57181394731353e-05 3.8272036082994e-79 2.85600280627803e-79
## HLA-DPA10103-DPB10201 6 0_DHX15 ERDYLEAAIRAVIQI 848.12 32 ERDYLEAAIRTVIQI 965.99 34 4 NM_001358 c.A1012G T C 0 0 24529097 24586177 4_24556416 294 143 YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL 1.35204 NA NA 0.657624898 NA NA NA 0.00305880395874908 4.08993140784102e-66 3.05206013940527e-66
Count the number of neoantigens of which thresholds are IC 50 of mutatnt peptides < 500 and IC 50 of wild-type peptides > 500.
[R]
print(Export_Summary_SNV(Input = Result_HLA2_SNV, Mut_IC50_th = 500, Wt_IC50_th = 500))
## Num_All_Alteration Num_Evaluated_Alteration Num_Alteration_Generating_NeoAg Num_All_Peptide Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 3 3 1 45 45 9
Results generated from indels.
[R]
print(head(Result_HLA1_INDEL_1))
HLA Pos Gene Evaluated_Mutant_Peptide_Core Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr NM_ID Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
HLA-A*02:01 1 0_UGT2B28 GIPMVGIPLV IYHGIPMVGIPLV 8158.7 12.6683 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
HLA-A*02:01 2 0_UGT2B28 YHGIPMVGIPLVL YHGIPMVGIPLVL 264.7 1.9668 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
HLA-A*02:01 3 0_UGT2B28 HGIPMVGIPLVL HGIPMVGIPLVLG 14185.4 18.6104 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
HLA-A*02:01 4 0_UGT2B28 GIPMVGIPLV GIPMVGIPLVLGS 13299.6 17.694 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
HLA-A*02:01 5 0_UGT2B28 IPMVGIPLVL IPMVGIPLVLGST 17674.7 22.4056 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
HLA-A*02:01 2 0_UGT2B28 GIPMVGIPLV YHGIPMVGIPLV 5439.5 9.9316 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
Count the number of neoantigens of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV(Input = Result_HLA1_INDEL_1, Mut_IC50_th = 500))
## Num_All_Alteration Num_Evaluated_Alteration Num_Alteration_Generating_NeoAg Num_All_Peptide Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 3 3 3 270 270 15
Count the number of neoantigens for each peptide of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV_perFragments(Input = Result_HLA1_INDEL_1, Mut_IC50_th = 500))
## EAIYHGIPMVGIPLVLGSTX-0_UGT2B28 QYYQRDELLAAIKKFHIKVATQX-1_COL12A1 IMEMARDFLPSLKNPFWKPSILPIFMYKHCSVQFSVRHGDVQTKVHX-2_SLCO1C1
## Num_Peptide_Per_Pep 30 48 192
## Num_Cond_Peptide_Per_Pep 30 48 192
## Num_Rest_Peptide_Per_Pep 4 2 9
## Num_Rest_Peptide_Per_Pep/Num_Cond_Peptide_Per_Pep 0.133 0.042 0.047
## -logP 0.414 0.483 1.035
Results generated from indels.
[R]
print(head(Result_HLA2_INDEL))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr NM_ID Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## HLA-DPA10103-DPB10201 3 0_UGT2B28 YHGIPMVGI EAIYHGIPMVGIPLV 682.35 28 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 EAIYHGIPMVGIPLFWDQPDNIAHMKAKGA EAIYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
## HLA-DPA10103-DPB10201 2 0_UGT2B28 YHGIPMVGI AIYHGIPMVGIPLVL 643.18 27 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 EAIYHGIPMVGIPLFWDQPDNIAHMKAKGA EAIYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
## HLA-DPA10103-DPB10201 1 0_UGT2B28 YHGIPMVGI IYHGIPMVGIPLVLG 799.71 31 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 EAIYHGIPMVGIPLFWDQPDNIAHMKAKGA EAIYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
## HLA-DPA10103-DPB10201 4 0_UGT2B28 PMVGIPLVL YHGIPMVGIPLVLGS 984.87 35 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 EAIYHGIPMVGIPLFWDQPDNIAHMKAKGA EAIYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
## HLA-DPA10103-DPB10201 3 0_UGT2B28 PMVGIPLVL HGIPMVGIPLVLGST 1262.77 40 4 NM_053039 Out_c.1186dupT - T 0 0 70146192 70160768 4_70156404 84 43 EAIYHGIPMVGIPLFWDQPDNIAHMKAKGA EAIYHGIPMVGIPLVLGSTX 0 NA NA 0 NA NA NA 0 0 0
## HLA-DPA10103-DPB10201 2 1_COL12A1 YQRDELLAA QYYQRDELLAAIKKF 528.36 23 6 NM_004370 Out_c.628delA T - 0 0 75794041 75915769 6_75899298 195 122 QYYQRDELLAAIKKIPYKGGNTMTGDAIDYLVK QYYQRDELLAAIKKFHIKVATQX 0 NA NA 0 NA NA NA 0 0 0
Count the number of neoantigens of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV(Input = Result_HLA2_INDEL, Mut_IC50_th = 500))
## Num_All_Alteration Num_Evaluated_Alteration Num_Alteration_Generating_NeoAg Num_All_Peptide Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 3 3 3 45 45 32
Count the number of neoantigens for each peptide of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV_perFragments(Input = Result_HLA2_INDEL, Mut_IC50_th = 500))
## EAIYHGIPMVGIPLVLGSTX-0_UGT2B28 QYYQRDELLAAIKKFHIKVATQX-1_COL12A1 IMEMARDFLPSLKNPFWKPSILPIFMYKHCSVQFSVRHGDVQTKVHX-2_SLCO1C1
## Num_Peptide_Per_Pep 5 8 32
## Num_Cond_Peptide_Per_Pep 5 8 32
## Num_Rest_Peptide_Per_Pep 5 7 20
## Num_Rest_Peptide_Per_Pep/Num_Cond_Peptide_Per_Pep 1 0.875 0.625
## -logP 0.46 0.529 1.081
Results generated from SVs.
[R]
print(head(Result_HLA1_SV))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr NM_ID Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## HLA-A*02:01 1 0_AAR2 YNSWEVGPKF DYNSWEVGPKFRE 41548.2 77.1323 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE 3.03498 NA NA NaN NA NA NA 3.91642729756511e-268 7.08393938415568e-164 7.08395743628947e-164
## HLA-A*02:01 2 0_AAR2 YNSWEVGPKF YNSWEVGPKFREQ 37159.3 60.6291 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE 3.03498 NA NA NaN NA NA NA 1.52762178578222e-239 4.85868009372317e-128 4.85869247518755e-128
## HLA-A*02:01 3 0_AAR2 NSWEVGPKFREQL NSWEVGPKFREQL 17541.5 22.2465 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE 3.03498 NA NA NaN NA NA NA 9.60616737856677e-112 1.07963066292279e-44 1.07963341416559e-44
## HLA-A*02:01 4 0_AAR2 WEVGPKFREQLK SWEVGPKFREQLK 41225.3 75.8035 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE 3.03498 NA NA NaN NA NA NA 4.97044636800253e-266 5.4416095168521e-161 5.44162338380631e-161
## HLA-A*02:01 5 0_AAR2 WEVGPKFREQLKL WEVGPKFREQLKL 30625.8 42.6216 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE 3.03498 NA NA NaN NA NA NA 5.57135466629207e-197 6.15612910885357e-89 6.15614479663127e-89
## HLA-A*02:01 6 0_AAR2 EVGPKFREQLKL EVGPKFREQLKLF 40083 71.2831 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE 3.03498 NA NA NaN NA NA NA 1.37345423305794e-258 3.56165011967455e-151 3.56165919589344e-151
Count the number of neoantigens of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV(Result_HLA1_SV, Mut_IC50_th = 500))
## Num_All_Alteration Num_Evaluated_Alteration Num_Alteration_Generating_NeoAg Num_All_Peptide Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 16 16 10 3120 3120 118
Count the number of neoantigens for each peptide of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV_perFragments(Result_HLA1_SV, Mut_IC50_th = 500))
## DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE-0_AAR2 GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG-1_SLC25A12 TMAEKRQLFIEMLYRLX-2_DTNB TDWLSDCCFHPSERCRCTLYGHTDSVNSIEFFP-3_SPAG16 ACLPGEEGTAERSCKRNLSTTTGSSERX-4_TMCC1 GQLRGLIPSSPQKTLECKQQKIILLRREMKETX-9_PDLIM3 GDQYIVDMANTKRTLLWTRPMTVILGKPFCVMPKQQKTAHIGFLQHIPRLSPKPCLPKLNLMMRKQRMSQNGKNVKFEESHLRAVCMSGRGMGQVWVFFLCSX-10_WDR70 LCPASRALEEKKGHELLGGPSLGAPRPGSQERTGENTAACQDHRFWAGQTAGCGRERIPCRRRQSAYQVDGIGINFTQNLYPPEX-11_EGFR LTPMPEGLSQQQDMLKNTSKGHPDRLPLQMALT-12_ARHGEF10 PGVQGKKVRKPSPTTSASSSSWTSAGTSWPAGRRTGTATSGTATTTSVWPGCGTRMWSTQWSSVPRSRSCCSRPATTPPSKPGAPHAPCASSRHLAHGLAPSSPGLPARGAEVCWVHWSHRDPLRTSPGSVAFSRAGEVEMLIAVTPX-13_NOTCH1 SRGRGNNNRKGREVTPL-14_UBAP2 IPSSQLAAKLLHMLTMRMLSKSATGRWX-15_RASGRP2 RKSPPEKKLRRYPPGQGATIGVDFMIKTVEINGE-16_GAB2 MSVIVLPQPDEVLNLVQSYVTLRVPLYVSYVFH-17_MTRF1 LWKCLRKPVLNDRNLQLHTDKGSFLKEKNKKLKKK-18_EVI2B RTFLQSTDPGDTGGVFEGSTLCPSDPAFSRTDDPX-19_IKZF3 NVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-20_IKZF3 DALTGHLRTHSGGVFEGSTLCPSDPAFSRTDDPX-21_IKZF3 FNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-22_IKZF3 EGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-23_IKZF3 GEGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-24_IKZF3 RDALTGHLRTHSGGVFEGSTLCPSDPAFSRTDDPX-25_IKZF3
## Num_Peptide_Per_Pep 57 237 24 51 90 120 540 432 51 810 30 90 57 51 63 132 126 126 132 126 132 132
## Num_Cond_Peptide_Per_Pep 57 237 24 51 90 120 540 432 51 810 30 90 57 51 63 132 126 126 132 126 132 132
## Num_Rest_Peptide_Per_Pep 0 6 6 0 0 1 39 3 0 41 0 11 0 2 1 2 4 4 4 1 1 4
## Num_Rest_Peptide_Per_Pep/Num_Cond_Peptide_Per_Pep 0 0.025 0.25 0 0 0.008 0.072 0.007 0 0.051 0 0.122 0 0.039 0.016 0.015 0.032 0.032 0.03 0.008 0.008 0.03
## -logP 0.782 1.496 0.391 0.759 0.644 0.759 2.37 1.956 0.759 3.405 0.391 0.644 0.782 0.759 0.805 0.805 0.782 0.782 0.805 0.782 0.805 0.805
Results generated from SVs.
[R]
print(head(Result_HLA2_SV))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr NM_ID Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## HLA-DPA10103-DPB10201 6 0_AAR2 WEVGPKFRE GIDYNSWEVGPKFRE 3510.19 65 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK 3.03498 NA NA NaN NA NA NA 2.44544417236296e-20 1.56757940967125e-137 1.56758340436286e-137
## HLA-DPA10103-DPB10201 5 0_AAR2 WEVGPKFRE IDYNSWEVGPKFREQ 3548.49 65 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK 3.03498 NA NA NaN NA NA NA 1.37675154589193e-20 1.56757940967125e-137 1.56758340436286e-137
## HLA-DPA10103-DPB10201 4 0_AAR2 WEVGPKFRE DYNSWEVGPKFREQL 3382.78 65 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK 3.03498 NA NA NaN NA NA NA 1.65333040189821e-19 1.56757940967125e-137 1.56758340436286e-137
## HLA-DPA10103-DPB10201 3 0_AAR2 WEVGPKFRE YNSWEVGPKFREQLK 3259.68 65 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK 3.03498 NA NA NaN NA NA NA 1.04781452055042e-18 1.56757940967125e-137 1.56758340436286e-137
## HLA-DPA10103-DPB10201 2 0_AAR2 WEVGPKFRE NSWEVGPKFREQLKL 3578.45 65 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK 3.03498 NA NA NaN NA NA NA 8.78382414821159e-21 1.56757940967125e-137 1.56758340436286e-137
## HLA-DPA10103-DPB10201 6 0_AAR2 KFREQLKLF SWEVGPKFREQLKLF 2000.52 50 20 NM_015511_NM_015906 In_AAR2_exon_TRIM33_exon G G]1:115005805] 0 0 34824338 34844863 20_34827929 0 0 MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFvcfLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK 3.03498 NA NA NaN NA NA NA 1.67100600273435e-10 5.85215328550208e-105 5.85216819865257e-105
Count the number of neoantigens of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV(Result_HLA2_SV, Mut_IC50_th = 500))
## Num_All_Alteration Num_Evaluated_Alteration Num_Alteration_Generating_NeoAg Num_All_Peptide Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 16 16 12 573 573 292
Count the number of neoantigens for each peptide of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_IndelSV_perFragments(Result_HLA2_SV, Mut_IC50_th = 500))
## GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK-0_AAR2 KRGDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGGAI-1_SLC25A12 RKTMAEKRQLFIEMLYRLX-2_DTNB GHTDWLSDCCFHPSERCRCTLYGHTDSVNSIEFFPFS-3_SPAG16 AAACLPGEEGTAERSCKRNLSTTTGSSERX-4_TMCC1 MKSCKRNLSTTTGSSERX-5_TMCC1 MVQRFSLRRQLSKSCKRNLSTTTGSSERX-6_TMCC1 PMQRKGSYCWDFEESCKRNLSTTTGSSERX-7_TMCC1 HNIRPKPFVIPGRSRTLECKQQKIILLRREMKETX-8_PDLIM3 IKGDQYIVDMANTKRTLLWTRPMTVILGKPFCVMPKQQKTAHIGFLQHIPRLSPKPCLPKLNLMMRKQRMSQNGKNVKFEESHLRAVCMSGRGMGQVWVFFLCSX-9_WDR70 AALCPASRALEEKKGHELLGGPSLGAPRPGSQERTGENTAACQDHRFWAGQTAGCGRERIPCRRRQSAYQVDGIGINFTQNLYPPEX-10_EGFR AILTPMPEGLSQQQDMLKNTSKGHPDRLPLQMALTEL-11_ARHGEF10 LKPGVQGKKVRKPSPTTSASSSSWTSAGTSWPAGRRTGTATSGTATTTSVWPGCGTRMWSTQWSSVPRSRSCCSRPATTPPSKPGAPHAPCASSRHLAHGLAPSSPGLPARGAEVCWVHWSHRDPLRTSPGSVAFSRAGEVEMLIAVTPX-12_NOTCH1 ESSRGRGNNNRKGREVTPL-13_UBAP2 WYIPSSQLAAKLLHMLTMRMLSKSATGRWX-14_RASGRP2 WLRKSPPEKKLRRYPPGQGATIGVDFMIKTVEINGEKV-15_GAB2 GTMSVIVLPQPDEVLNLVQSYVTLRVPLYVSYVFHSP-16_MTRF1 IVLWKCLRKPVLNDRNLQLHTDKGSFLKEKNKKLKKKNK-17_EVI2B RCRTFLQSTDPGDTGGVFEGSTLCPSDPAFSRTDDPX-18_IKZF3 SFNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-19_IKZF3 SGEGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-20_IKZF3 DSGEGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-21_IKZF3 QRRDALTGHLRTHSGGVFEGSTLCPSDPAFSRTDDPX-22_IKZF3 ISFNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-23_IKZF3
## Num_Peptide_Per_Pep 14 44 4 13 15 3 14 15 20 90 72 13 135 5 15 14 13 15 22 21 21 22 22 22
## Num_Cond_Peptide_Per_Pep 14 44 4 13 15 3 14 15 20 90 72 13 135 5 15 14 13 15 22 21 21 22 22 22
## Num_Rest_Peptide_Per_Pep 0 19 4 0 0 0 9 0 10 55 24 0 94 0 15 5 6 11 10 17 12 12 13 18
## Num_Rest_Peptide_Per_Pep/Num_Cond_Peptide_Per_Pep 0 0.432 1 0 0 0 0.643 0 0.5 0.611 0.333 0 0.696 0 1 0.357 0.462 0.733 0.455 0.81 0.571 0.545 0.591 0.818
## -logP 0.874 1.588 0.437 0.851 0.69 0.414 0.667 0.69 0.805 2.416 2.002 0.851 3.451 0.437 0.69 0.874 0.851 0.897 0.851 0.828 0.828 0.851 0.851 0.851
Results generated from RNA sequences.
[R]
print(head(Result_HLA1_Seq))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr NM_ID ReadingFrame SequenceNumber Chrs NM_IDs GeneIDs Exon_Starts Exon_Ends GroupID NumOfPeptides NumOfStops Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## HLA-A*02:01 1 0_atggcagaag MAEDDPYLGRPEK MAEDDPYLGRPEK 34529.5 52.6059 0 1 1 chr4;chr4 NM_001165412;NM_003998 NFKB1;NFKB1 103422515;103422515 103538459;103538459 0_1 27 0 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## HLA-A*02:01 2 0_atggcagaag AEDDPYLGRPEKM AEDDPYLGRPEKM 37395.3 61.456 0 1 1 chr4;chr4 NM_001165412;NM_003998 NFKB1;NFKB1 103422515;103422515 103538459;103538459 0_1 27 0 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## HLA-A*02:01 3 0_atggcagaag YLGRPEKMF EDDPYLGRPEKMF 41328 76.2274 0 1 1 chr4;chr4 NM_001165412;NM_003998 NFKB1;NFKB1 103422515;103422515 103538459;103538459 0_1 27 0 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## HLA-A*02:01 4 0_atggcagaag YLGRPEKMFH DDPYLGRPEKMFH 42864.6 82.5363 0 1 1 chr4;chr4 NM_001165412;NM_003998 NFKB1;NFKB1 103422515;103422515 103538459;103538459 0_1 27 0 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## HLA-A*02:01 5 0_atggcagaag YLGRPEKMFHL DPYLGRPEKMFHL 3345.9 7.5921 0 1 1 chr4;chr4 NM_001165412;NM_003998 NFKB1;NFKB1 103422515;103422515 103538459;103538459 0_1 27 0 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## HLA-A*02:01 6 0_atggcagaag YLGRPEKMFHL PYLGRPEKMFHLD 19715.7 24.819 0 1 1 chr4;chr4 NM_001165412;NM_003998 NFKB1;NFKB1 103422515;103422515 103538459;103538459 0_1 27 0 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
Count the number of neoantigens for each peptide of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_Fragments(Result_HLA1_Seq, Mut_IC50_th = 500))
## [[1]]
## atggcagaag
## Num_Peptide_Per_Grp 63.000
## Num_Cond_Peptide_Per_Grp 63.000
## Num_Rest_Peptide_Per_Grp 5.000
## Num_Rest_Peptide_Per_Grp / Num_Cond_Peptide_Per_Grp 0.079
## -logP 0.621
## [[2]]
##
## Num_Peptide_Per_NM 63.000
## Num_Cond_Peptide_Per_NM 63.000
## Num_Rest_Peptide_Per_NM 5.000
## Num_Rest_Peptide_Per_NM / Num_Cond_Peptide_Per_NM 0.079
## -logP 0.621
## [[3]]
## MAEDDPYLGRPEKMFHLDPSLTHTIFN-0_atggcagaag-0_1
## Num_Peptide_Per_Pep 63.000
## Num_Cond_Peptide_Per_Pep 63.000
## Num_Rest_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.079
## -logP 0.621
Results generated from RNA sequences.
[R]
print(head(Result_HLA2_Seq))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr NM_ID ReadingFrame SequenceNumber Chrs NM_IDs GeneIDs Exon_Starts Exon_Ends GroupID NumOfPeptides NumOfStops Wt_Peptide Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## HLA-DPA10103-DPB10201 5 0_atggcagaag GRPEQMFHL DDPYLGRPEQMFHLI 2116.65 55 0 1 1 chr4;chr4;chr19;chr4 NM_001165412;NM_003998;NM_005178;NM_001319226 NFKB1;NFKB1;BCL3;NFKB1 103422515;103422515;45251964;103423090 103538459;103538459;45263301;103538459 0_1 27 1 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## HLA-DPA10103-DPB10201 4 0_atggcagaag GRPEQMFHL DPYLGRPEQMFHLIL 938.03 34 0 1 1 chr4;chr4;chr19;chr4 NM_001165412;NM_003998;NM_005178;NM_001319226 NFKB1;NFKB1;BCL3;NFKB1 103422515;103422515;45251964;103423090 103538459;103538459;45263301;103538459 0_1 27 1 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## HLA-DPA10103-DPB10201 6 0_atggcagaag EQMFHLILL PYLGRPEQMFHLILL 285.69 14 0 1 1 chr4;chr4;chr19;chr4 NM_001165412;NM_003998;NM_005178;NM_001319226 NFKB1;NFKB1;BCL3;NFKB1 103422515;103422515;45251964;103423090 103538459;103538459;45263301;103538459 0_1 27 1 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## DRB1_1302 3 0_atggcagaag YLGRPEQMF DDPYLGRPEQMFHLI 5199.08 90 0 1 1 chr4;chr4;chr19;chr4 NM_001165412;NM_003998;NM_005178;NM_001319226 NFKB1;NFKB1;BCL3;NFKB1 103422515;103422515;45251964;103423090 103538459;103538459;45263301;103538459 0_1 27 1 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## DRB1_1302 4 0_atggcagaag GRPEQMFHL DPYLGRPEQMFHLIL 3820.74 80 0 1 1 chr4;chr4;chr19;chr4 NM_001165412;NM_003998;NM_005178;NM_001319226 NFKB1;NFKB1;BCL3;NFKB1 103422515;103422515;45251964;103423090 103538459;103538459;45263301;103538459 0_1 27 1 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
## DRB1_1302 3 0_atggcagaag GRPEQMFHL PYLGRPEQMFHLILL 3239.61 80 0 1 1 chr4;chr4;chr19;chr4 NM_001165412;NM_003998;NM_005178;NM_001319226 NFKB1;NFKB1;BCL3;NFKB1 103422515;103422515;45251964;103423090 103538459;103538459;45263301;103538459 0_1 27 1 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX MAEDDPYLGRPEQMFHLILL NA NA NA NA NA NA NA
Count the number of neoantigens for each peptide of which threshold is IC 50 of mutatnt peptides < 500.
[R]
print(Export_Summary_Fragments(Result_HLA2_Seq, Mut_IC50_th = 500))
## [[1]]
## atggcagaag
## Num_Peptide_Per_Grp 3.000
## Num_Cond_Peptide_Per_Grp 3.000
## Num_Rest_Peptide_Per_Grp 1.000
## Num_Rest_Peptide_Per_Grp / Num_Cond_Peptide_Per_Grp 0.333
## -logP 0.460
## [[2]]
##
## Num_Peptide_Per_NM 3.000
## Num_Cond_Peptide_Per_NM 3.000
## Num_Rest_Peptide_Per_NM 1.000
## Num_Rest_Peptide_Per_NM / Num_Cond_Peptide_Per_NM 0.333
## -logP 0.460
## [[3]]
## MAEDDPYLGRPEQMFHLILL-0_atggcagaag-0_1
## Num_Peptide_Per_Pep 3.000
## Num_Cond_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.333
## -logP 0.460