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I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with -qseqid -sacc -qlen -slen -length -nident -pident -evalue -stitle and I want to set the evalue less than 1e-10. Here is my code :

#!/usr/bin/env bash
blastp -query Trinity.fasta.transdecoder.pep \
    -db swissprot \
    -outfmt "6 qseqid sacc qlen slen length nident pident evalue stitle" -evalue 1e-10 1>Predict.txt \
    2>wrongPredicted.err

However this is the first several lines of output I got in the txt file :

TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E0  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964D9  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P53472  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoskeletal 1A; AltName: Full=Actin, cytoskeletal IA; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P92179  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E1  400     376     376     363     96.54   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E2  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P69004  400     376     376     364     96.81   0.0     RecName: Full=Actin-15B; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   O17320  400     376     376     361     96.01   0.0     RecName: Full=Actin

The problem is that all the evalue is 0.0 for some reasons, cuz what I want is something like this :

TRINITY_DN8_c0_g1_i1 Q5ZKK7 283 788 64 53 82.81 1e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q7ZVV1 283 782 64 53 82.81 3e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q1RMT1 283 782 64 52 81.25 6e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q5RA62 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q60HG1 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3

The 8th column should be valid evalue. Need some help! Thank you!

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    $\begingroup$ Very low e values are rounded to zero, so that’s a valid output. $\endgroup$
    – acvill
    Nov 13, 2021 at 12:57
  • $\begingroup$ Welcome to Biology.SE! Please take the tour and then go through the help center pages starting with How to Ask questions effectively on this site. In particular, this question seems like it might be a better fit for Bioinformatics, but please do not crosspost, instead request migration after consulting that sites help and checking for duplicates. $\endgroup$
    – tyersome
    Nov 14, 2021 at 18:04

1 Answer 1

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  • 0 is a valid e-value. It is the strongest e-value you can get.
  • the sequence identifier in a FASTA file (and thus what BLAST uses) is "everything up to the first space". If what you have behind "::" is indeed useless, you should remove it from your query before submitting it.

FWIW, my lab makes SequenceServer, a powerful graphical interface for running BLAST. It enables you to run BLAST in the cloud or on your local computer.

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  • $\begingroup$ Good answer, but three links to your own application? Really! $\endgroup$
    – David
    Dec 8, 2021 at 20:12
  • $\begingroup$ Hi @David - Sorry I didn't mean to cause offence. I'm quite proud of what our app has accomplished: SequenceServer helps me and 1000s of others perform and interpret BLAST analyses every week. Anyhow, I've removed 1 of the 2 links to the app. $\endgroup$ Dec 10, 2021 at 10:13

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