---
name: "bp_find-blast-matches"
section: "1p"
platform: "linux"
package: "bioperl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bp_find-blast-matches"
---

# bp\_find-blast-matches(1p)

extract DNA sequences based on BLAST hits

## 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