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BP_FIND-BLAST-MATCHES(User Contributed Perl DocumentatBP_FIND-BLAST-MATCHES(1)

NAME
       bp_find-blast-matches.pl	- extract DNA sequences	based on BLAST hits

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

OPTIONS
   Mandatory:
       -blast
	   BLAST output	file to	read from. The alignment should	use the	file
	   specified by	'-fasta' option	ideally

       -fasta
	   FASTA file to read from. This is where the sequence will be
	   extracted from

   Optional:
       -h  Displays this help message

       -e  Maximum e-value for matches (0.01 by	default)

       -p  Number of base pairs	of 5' region to	be included with the sequence

       -5  Number of base pairs	of 5' region only, excluding the regular
	   sequence

       -3  Number of base pairs	of 3' region only, excluding the regular
	   sequence

       -n  Number of top hits to display, starting with	the best hit

       -o  Exact match to display (this	option can't be	used in	conjunction
	   with	'-n'

       -header
	   The FASTA header to display instead of the default

DESCRIPTION
       This script takes a BLAST output	file and a FASTA file as 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:
       find-blast-matches.pl -blast BLAST_FILE -fasta FASTA_FILE

       It parses through the BLAST file	to check for high quality matches,
       which are then searched for in the FASTA	file.  The sequence may	vary
       from you	candidate sequence, hence the BLAST search prior.

       The sequence from the FASTA file	is then	displayed to STDOUT.  Optional
       arguments can be	used, such as to extract the 5'	or 3' region.

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

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	 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 to help us 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

EDIT HISTORY
       2014-08-04 - Gabriel Abud
	   First features added

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

perl v5.32.1			  2019-12-07	      BP_FIND-BLAST-MATCHES(1)

NAME | SYNOPSIS | OPTIONS | DESCRIPTION | AUTHOR | FEEDBACK | EDIT HISTORY | DEPENDANCIES

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