NAME

bgrep - Wrapper for several suffix array tools

VERSION

This document describes bgrep version 0.8.5

SYNOPSIS

  # to create a database
  bgrep --backend Vmatch --database Data.fa --datapath data --createdb

  # to search
  bgrep [ Options ] --query_file Query.fa --database Data.fa  --datapath data

    --query_file    A Fasta file with the query sequences.
    --database      A Fasta database.

OPTIONS

--help

Brief help message.

--man

Full documentation

--backend b

The back-end tool. Agrep, GUUGle, Hypa and Vmatch are supported.

--mismatches n

The number of mismatches.

--editdistance n

The allowed edit distance.

--insertions n

The number of insertions.

--deletions n

The number of deletions.

--query_length n

Report all matches of length of at least n.

--reverse_complement

Searches for the reverse complement.

--direct_and_rev_com

Searches for direct matches and the reverse complement.

--upstream n

Display n nucleotides/AAs upstream the match.

--downstream n

Display n nucleotides/AAs downstream the match.

--sort s

Sets sort mode to s.

--maxhits n

Display only the n (best) hits.

--datapath p,

Generate suffix arrays in path p. Default is 'data'

--showdesc n,

Vmatch only (see manual). Is faster because it extracts all data directly out of the vmatch output. Otherwise, vsubseqselect is called for every hit.

--hxdrop n

Vmatch only (see manual). Specifies the xdrop value for hamming distance extension.

--exdrop n

Vmatch only (see manual). Specifies the xdrop value for edit distance extension.

--no_alignments

Don't calculate alignments with EMBOSS.

DESCRIPTION

Bio-Grep is a collection of Perl modules for searching in Fasta files. It is programmed in a modular way. There are different backends available. You can filter search results.

bgrep is an example of how to use this library.

BUGS AND LIMITATIONS

No bugs have been reported.

Please report any bugs or feature requests to bug-bio-grep@rt.cpan.org, or through the web interface at http://rt.cpan.org.

SEE ALSO

perldoc Bio::Grep

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENCE AND COPYRIGHT

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER OF WARRANTY

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