Find_novel_viruses_C_novel_cov
ababaian edited this page Jul 15, 2021
·
1 revision
DIAMOND search results
SRR2976063_NODE_10_length_227_cov_1.883117
ERR3994223.Epsy.StypNV 76%
Microassembly:
>SRR2976063_NODE_10_length_227_cov_1.883117
CGCCTATTTCTTTACTCCAGTATGTACGAACATGGTGATTTGGACTCTGCTTCCACGCTA
TTGTTCGAGCATATGCAACACACATGCCCTCTGATGATTCTTTCAGATGACGGCGTTGCT
GGACCTTTAACTGACGACCCAACTGCATGCTGTCTTGATGATTTTAAAGCTACGCTGTAC
TACCAGAACAACGTATATCTTTCTGATGAAAAGTGCTGACCTTGCTA
>SRR2976063_NODE_10_length_227_cov_1.883117_translated
EHMQHTCPLMILSDDGVAGPLTDDPTACCLDDFKATLYYQNNVYLSDEKC
- SRA
- BLAST 58.57% to PSNV (will expire)
DIAMOND:
SRR13002565_NODE_2_length_242_cov_0.911243
QEG08237.1.PsNV 72.7 1.55E-34
Microassembly:
>SRR13002565_NODE_2_length_242_cov_0.911243
GGTCCATGTATGTAAATATTACGATACAGATTATGTACGAAAGAACGGTTGGCAGCGGCT
GTGTTTTGAATAGCCTTGTTAACAGAAGTGGTAACAACCTGAAAGAGGTTGAAAGCACTG
TTAGCATAGGCCGTAGTTGAATCACCACTACTAGTACCACCGGGTTTCCTAAAGAAACTA
CCGTTAACGACACAAGTTTCTGAAAGAACTTGAGACATTTCGTTAGCGAGTCTGTACTTC
TT
>SRR13002565_NODE_2_length_242_cov_0.911243_translated
MSQVLSETCVVNGSFFRKPGGTSSGDSTTAYANSAFNLFQVVTTSVNKAIQNTAAANRSF
VHNLYRNIYIHG
- SRA
- BLAST 72% to PsNV
DIAMOND:
SRR5224039_NODE_1_length_291_cov_1.289256
QEG08237.1.PsNV 74.4 4.35E-41
Microassembly:
>SRR5224039_NODE_1_length_291_cov_1.289256
GTTCATTGGTAGTGTTGTTTTGAAGAGGCCAGTCGCGACGGACTATAGAGTCAATAGCAC
TGGTTATAACCTGAAATAAGTTAAAAGCGGAATTGGCGTAAGCGGTAGTGCCGTCACCTG
AGGAAGTACCCCCAGGTTTACGGTAAAGGTAACCGTTCACTAGACAAGTCTCGCTAAGAA
CCTGTTGCATTTCATTTGCAAGGCGATACAACTTATCAGGGTGCTGACAACAGTCAATGT
GCTTATTCAGAAATAGCCAAGCAGCAGACTGACGTAAGAGGTTAGGCATGG
>SRR5224039_NODE_1_length_291_cov_1.289256_translated
MPNLLRQSAAWLFLNKHIDCCQHPDKLYRLANEMQQVLSETCLVNGYLYRKPGGTSSGDG
TTAYANSAFNLFQVITSAIDSIVRRDWPLQNNTTNE
- SRA BLAST 75% to PsNV: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=DY3HADZW013 (edited)
DIAMOND:
SRR2290960_NODE_1_length_273_cov_1.803571
77.8%
Microassembly:
>SRR2290960_NODE_1_length_273_cov_1.803571
TAAGTACTCTATATCCAGTAAAGCTAGGGCTCGTACTGTGGCAGGTGTTTCTATTCTTTC
AACTGCCCTTAATCGTATGACTCATCAGCATTTACTTAAAGATATAGCAGCTGCCAGGGA
TAAAACTGTTTGCATTGGCACTCCTAAGTTTTATGGTAATTGGCACCTAATGATGTCACG
CTTTTTGGACGACAAACCTCGTCGTTTGATAGGTTGGGACTACCCTAAGTGTGACCGTTC
CATGCCTAACCTTATTCGCATGGCATCGTGTAT
>SRR2290960_NODE_1_length_273_cov_1.803571_translated
KYSISSKARARTVAGVSILSTALNRMTHQHLLKDIAAARDKTVCIGTPKFYGNWHLMMSR
FLDDKPRRLIGWDYPKCDRSMPNLIRMASC
- SRA
- BLAST 72% to PsNV
DIAMOND:
SRR6281441_NODE_69_length_424_cov_0.950166
QEG08237.1.PsNV 58.8
Microassembly:
>SRR6281441_NODE_69_length_424_cov_0.950166
AGCTCACACTGCGTCTTCAGTACCAACTATTGATACTCGTACAGACATTTATTGTGCTGG
TTCCAATCGTATTGTTCCAGGAAAGATACTTAAGCCTGCTAATATTGACTTTGCTTTTGT
AGAATTTGCTAAAAAGACTCTACTCTTTGAAGGCTCTCCTATAAAACTAAGTCATTTCTT
CTTTCTTGCCAATCGTGACTCTACTATTAAGGATTTTGACTATTATCGTTATAATATACC
CACAGTACTTGATATTAAACAGTTCCTCTTTACATACCAGGTTGTTTGTAAATATTTTGA
TGTTTACAATGCTGGATGTATATGTAGTTCTTCTGTTGTAGTTAATAACCCCAAGAAGTC
TGCCGGCTTTCCATTCAATATGTTTGGTTGTGCCGATGAAGTTCTTGACTATTTAGGACA
TGAC
>SRR6281441_NODE_69_length_424_cov_0.950166_translated
AHTASSVPTIDTRTDIYCAGSNRIVPGKILKPANIDFAFVEFAKKTLLFEGSPIKLSHFF
FLANRDSTIKDFDYYRYNIPTVLDIKQFLFTYQVVCKYFDVYNAGCICSSSVVVNNPKKS
AGFPFNMFGCADEVLDYLGHD
- SRA
- BLAST: 57% to PsNV
DIAMOND:
ERR3588795_NODE_755_length_225_cov_1.013158
SRR10917299.TparNV 74.3%
Microassembly:
>ERR3588795_NODE_755_length_225_cov_1.013158
CGGCATAGAACGATCACATTTAGGGTAATCCCAACCAAACAAGGTACGGCTGTGCCCGTC
ATTAAAACGAAGAAGCATCCTGTGCCAGTGTCCATAGAATTTAGGAGTACCTATAACACA
TGTTTGGTCTCTACCTGCAGCTATATTTTTCAACAGTTTCTGATGACAGCAACGGTTTAA
AATAGTAGACAAAATGCTTACACCAGCAATGGTGCGAGCTCTGGG
>ERR3588795_NODE_755_length_225_cov_1.013158_translated
PRARTIAGVSILSTILNRCCHQKLLKNIAAGRDQTCVIGTPKFYGHWHRMLLRFNDGHSR
TLFGWDYPKCDRSMP
- SRA
- BLAST 74% to PsNV
DIAMOND:
SRR1185235_NODE_1_length_372_cov_2.241486
SRR2418623.MeLV 63.9%
Microassembly:
>SRR1185235_NODE_1_length_372_cov_2.241486
GGTAGTTATAAATTGAATGATGTTAAAAACAGAATTAGCGGGTGCTGTAGTTGCATCACC
GCTAGAAGTACCACCAGGTTTGGTATAAAAAGAACCATTAACAAAAACGTATTCGTTAAT
AACCTGAGCGTGTTCGTTGACTAATCTATAAAATTTATCAGAATTAGAACAACAATCTTT
GTGTGATCGTAATAATGTTAAACATGAAGCTACACGAATAATATTAGGCATAGCACGATC
ACATTTAGGATAATCCCATCCATAGAGAACAGGGTTGTTTATATTGGTAATCATACGTTT
GAGCATAGAATCCCAACCACCGTAATATTTAGTTCTACCTATAACAATGGTAGCATCAGG
TGTAGAAGTAAT
>SRR1185235_NODE_1_length_372_cov_2.241486_translated
ITSTPDATIVIGRTKYYGGWDSMLKRMITNINNPVLYGWDYPKCDRAMPNIIRVASCLTL
LRSHKDCCSNSDKFYRLVNEHAQVINEYVFVNGSFYTKPGGTSSGDATTAPANSVFNIIQ
FITT
DIAMOND:
SRR7719395_NODE_115_length_207_cov_1.639241
QEG08237.1.PsNV 41.5%
Microassembly:
>SRR7719395_NODE_115_length_207_cov_1.639241
CCAACATCTACTATTAAAGTTCGTAACCCCCATAAATCTTCAGGCATACCTTACCGTAAT
TACGGTGATGCTGAATTTATGCGTGATTTATATGGTAAAGACCGTGATAAAATAACTTTA
CACAAAACTCATTCCGCTGATCCATCTTTTACGCTTGTTATAAATAAAGTAGCTATATCT
ACAAAACCACGTGACCGTACTATTTTA
>SRR7719395_NODE_115_length_207_cov_1.639241_translated
PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGKDRDKITLHKTHSADPSFTLVINKVAIS
TKPRDRTIL
- SRA
- BLAST 98% to AC Meson-like:
Aphis citricidus meson-like virus
Query 1 PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGKDRDKITLHKTHSADPSFTLVINKVAIS 180
PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGK+RDKITLHKTHSADPSFTLVINKVAIS
Sbjct 509 PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGKERDKITLHKTHSADPSFTLVINKVAIS 568
Query 181 TKPRDRTIL 207
TKPRDRTIL
Sbjct 569 TKPRDRTIL 577
DIAMOND:
SRR8946811_NODE_17_length_330_cov_0.894942
QEG08237.1.PsNV 39.7%
Microassembly:
>SRR8946811_NODE_17_length_330_cov_0.894942
CTGCGTCCAGCTTCGCTTTTGTTGGAATTAATAGCAAGGATTGTGCGGTCGCGATGCTTT
GTACTGAGGGCAACTTTATTGATTACAAGGGTGAGATTTTGATCAGAAGAGTGTTGTTTG
TGTGCAACAATTTTGTCTCGGTGTTCTCCATATATGTCTCGTATAAATTGGCCATCTCCG
TGATTTCTATAGGGAATGCCTGAGGATTTATGTTTATTGCGAATTTTGACAGAGGAGACG
GGGGTGACACAATTAGGTTTACCATCTGAAGTGCATACTTCGCTGCGCAATAAAAATGTA
ACAGCTTCAACAATAAAAAGTAGGTTGACA
>SRR8946811_NODE_17_length_330_cov_0.894942_translated
VNLLFIVEAVTFLLRSEVCTSDGKPNCVTPVSSVKIRNKHKSSGIPYRNHGDGQFIRDIY
GEHRDKIVAHKQHSSDQNLTLVINKVALSTKHRDRTILAINSNKSEAGR
- SRA
- BLAST 66.97% to AC Meson-like:
Aphis citricidus meson-like virus -
Query 329 VNLLFIVEAVTFLLRSEVCTSDGKPNCVTPVSSVKIRNKHKSSGIPYRNHGDGQFIRDIY 150
VNLL E V LRS V +DGKP+ V P S++K+RN HKSSGIPYRN+GD +F+RD+Y
Sbjct 480 VNLLMCYEYVLHKLRSRVVATDGKPSIVLPTSTIKVRNPHKSSGIPYRNYGDAEFMRDLY 539
Query 149 GEHRDKIVAHKQHSSDQNLTLVINKVALSTKHRDRTILAINSNKSEAGR 3
G+ RDKI HK HS+D + TLVINKVA+STK RDRTILAINSNKSE GR
Sbjct 540 GKERDKITLHKTHSADPSFTLVINKVAISTKPRDRTILAINSNKSECGR 588
- Accessing Serratus Data
- Data Types
- Sequence References
- Running Serratus
- Finding Novel Viruses (tutorials)
- Papers using Serratus
- Containers
- Summarizer usage
- Cloud Budgeting
- Data Policy
- Serratus Annotation
- Serratus Assembly
- FLOM reference
- Proteome guided assembly for high divergence low coverage genomes
- PRICE de novo assembly
- Taxonomy case study of misannotated Genbank entry
- Taxonomy prediction
- Tree placement and taxonomy data
- Design of nucleotide summarizer scoring and-depth estimates
- Cov-phylogenetic-tree-quality-by-monophylicity
- Running a Treesearch
- Finding-transfer---recombination-events-in-the-Spike-protein
- Serratus SQL Database Management
- Trees-and-alignments-for-Ribovirus-orders-and-families
- Viral-contigs-containing-RdRP