This code is associated with the paper from Fernandes et al., "Discovery of surrogate agonists for visceral fat Treg cells that modulate metabolic indices in vivo". eLife, 2020. http://doi.org/10.7554/eLife.58463
This code is associated with the paper from Mendoza et al., "Recognition landscape interrogation of a conserved HIV specific TCR reveals distinct bacterial peptide cross-reactivity". eLife, 2020. http://doi.org/10.7554/eLife.58128
scripts for processing NGC data for TCR recognition of peptide sequences and prediction List of Programs for Deep sequencing fasta2pfam.pl <input.fasta> <output.pfam> This program quickly and easily converts a fasta sequence file to pfam format. pfam2fasta.pl <input.pfam> This program will convert a pfam sequence file to fasta format. trimpfam.pl <input.pfam> startpos endpos countUniques-generic.pl <input.pfam> alignmentFrequencies.pl <input.pfam> sortALLMSA.pl <input.pfam> This script will trim the sequences in your pfam sequence file i.e. sequences that are length of 100 and you want only positions 10 to 20, running this script will do this for you. This script will generate an output of unique sequences along with a statistics file. This script will give you positional frequencies for an alignment. Output is a csv file. This script provides library frequency statistics on a positional basis and important for co-variation analysis. This scripts generates a subdirectory of the sequence file and the Matlab scripts need to access this directory for visualization and analysis. Matlab script must be edited for each sequence file. UniquesPfamtoIndividualPfam.pl <input.pfam>
bin_uniques.pl <input_1.pfam> ... <input_N.pfam> This script generates a csv file listing data of unique sequences in all the inputted sequence files for generating a Vinn diagram type analysis. AlignNRtoLib_tophits.pl <input_Library_sequences.pfam> <input_NR_hits.pfam> X This script align Library sequences to NR hits and outputs the hits NR hits that have a sequence in your library with a greater than X sequence identity. AlignNRtoLib_Matrix.pl <input_Library_sequences.pfam> <input_NR_hits.pfam> This script align Library sequences to NR hits and outputs a matrix of sequence identities. This can get very large dependent on number of sequences in each input file. perl /usr/local/bin/deepsequence/AlignHitstoOneSequence.pl GAGseq.txt NRhits_17_7.txt > percentIDtoGAT.txt This will read out of percent identity of the NRhits list to your single sequence. cutoffpctsequences.pl Round# Pct# You must run this from where your uniques_stats.csv file is located. This will output the sequences required to reach Pct# of reads.
List of Programs for Deep sequencing fasta2pfam.pl <input.fasta> <output.pfam> This program quickly and easily converts a fasta sequence file to pfam format. pfam2fasta.pl <input.pfam> This program will convert a pfam sequence file to fasta format. trimpfam.pl <input.pfam> startpos endpos countUniques-generic.pl <input.pfam> alignmentFrequencies.pl <input.pfam> sortALLMSA.pl <input.pfam> This script will trim the sequences in your pfam sequence file i.e. sequences that are length of 100 and you want only positions 10 to 20, running this script will do this for you. This script will generate an output of unique sequences along with a statistics file. This script will give you positional frequencies for an alignment. Output is a csv file. This script provides library frequency statistics on a positional basis and important for co-variation analysis. This scripts generates a subdirectory of the sequence file and the Matlab scripts need to access this directory for visualization and analysis. Matlab script must be edited for each sequence file. UniquesPfamtoIndividualPfam.pl <input.pfam>
bin_uniques.pl <input_1.pfam> ... <input_N.pfam> This script generates a csv file listing data of unique sequences in all the inputted sequence files for generating a Vinn diagram type analysis. AlignNRtoLib.pl <input_Library_sequences.pfam> <input_NR_hits.pfam> X This script align Library sequences to NR hits and outputs the hits NR hits that have a sequence in your library with a greater than X sequence identity. AlignNRtoLib_Matrix.pl <input_Library_sequences.pfam> <input_NR_hits.pfam> This script align Library sequences to NR hits and outputs a matrix of sequence identities. This can get very large dependent on number of sequences in each input file. cutoffpctsequences.pl Round# Pct# You must run this from where your uniques_stats.csv file is located. This will output the sequences required to reach Pct# of reads.