BP_FIN...MATCHES(1p)

💅 BP_FIN...MATCHES(1p) — bestie edition 💅

okay so this is the manual page for bp_find-blast-matches.pl, living in section 1p of the User Contributed Perl Documentation, and it's literally the tool you want when your DNA sequences need to be found via their BLAST hits. no cap, it's giving bioinformatics main character energy 🧬✨

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🌸 NAME 🌸

bp_find-blast-matches.pl — pull out DNA sequences based on BLAST hits 🦋

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✨ SYNOPSIS ✨

bp_find-blast-matches.pl [-h -e -p -5 -n -o -3 -header] -blast
<BLAST_FILE> -fasta <FASTA_FILE>

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👑 OPTIONS 👑

🎀 Mandatory:

• -blast — the BLAST output file you're reading from. ideally the alignment should use the file you named with the -fasta option, okay? that's the vibe.
• -fasta — the FASTA file you're reading from. this is where the sequence actually gets extracted from, periodt.

💖 Optional:

• -h — shows you this help message. iconic of her.
• -e — maximum e-value for matches (0.01 by default).
• -p — how many base pairs of the 5' region get included along with the sequence.
• -5 — how many base pairs of the 5' region only, excluding the regular sequence.
• -3 — how many base pairs of the 3' region only, excluding the regular sequence.
• -n — how many top hits to display, starting with the best hit.
• -o — exact match to display. lowkey important: this option can't be used in conjunction with -n.
• -header — the FASTA header to display instead of the default one.

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🌈 DESCRIPTION 🌈

so this script takes a BLAST output file and a FASTA file as its arguments, given after the -blast and -fasta options respectively. the BLAST output file should have been generated with your sequence of interest and the FASTA file supplied as an argument. example, bestie:

find-blast-matches.pl -blast BLAST_FILE -fasta FASTA_FILE

it parses through the BLAST file to check for high quality matches, which then get searched for in the FASTA file. the sequence may vary from your candidate sequence — hence the BLAST search beforehand, iykyk.

then the sequence from the FASTA file gets displayed to STDOUT. optional arguments can be used, like extracting the 5' or 3' region. slay. 💅

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🫶 AUTHOR 🫶

Gabriel Abud - <gabriel.jabud-at-gmail.com>

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💬 FEEDBACK 💬

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via email or the web:

https://github.com/bioperl/bioperl-live/issues

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📝 EDIT HISTORY 📝

• 2014-08-04 - Gabriel Abud
  • First features added

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🧚 DEPENDANCIES 🧚

Getopt::long, Pod::Usage, Bio::SearchIO, Bio::Seq, Bio::SeqIO, File::Basename

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and that's the whole page, bestie 💖 this one shipped with perl v5.32.1 and was dated 2021-08-15, signed off as BP_FIN...MATCHES(1p) — go extract some sequences, you got this 🫶✨🎀