Bio::Grep Perl extension for searching in DNA and Protein sequences
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Bio::Grep Tags

Perl module perl protein DNA search DNA sequence search Protein sequence

Bio::Grep Description

Perl extension for searching in DNA and Protein sequences Bio::Grep is a Perl extension for searching in DNA and Protein sequences.SYNOPSIS use Bio::Grep; my $sbe = Bio::Grep->new('Vmatch'); # define the location of the suffix arrays $sbe->settings->datapath('data'); mkdir($sbe->settings->datapath); # now generate a suffix array. you have to do this only once. $sbe->generate_database({ file => 'ATH1.cdna', description => 'AGI Transcripts', }); # search in this suffix array $sbe->settings->database('ATH1.cdna'); # search for the reverse complement and allow 2 mismatches $sbe->settings->query('UGAACAGAAAG'); $sbe->settings->reverse_complement(1); $sbe->settings->mismatches(2); # or you can use Fasta file with queries # $sbe->settings->query_file('Oligos.fasta'); # $sbe->search(); # Alternatively, you can specify the settings in the search call. # This also resets everything except the paths and the database # (because it is likely that they don't change when search is called # multiple times) $sbe->search( { query => 'AGAGCCCT', reverse_complement => 1, mismatches => 1, }); my @ids; # output some informations! while ( my $res = $sbe->next_res ) { print $res->sequence->id . " "; print $res->alignment_string() . " "; push @ids, $res->sequence_id; } # get the gene sequences of all matches as Bio::SeqIO object. # (to generate a Fasta file for example) my $seqio = $sbe->get_sequences(@ids);Bio-Grep is a collection of Perl modules for searching in DNA and Protein sequences. It supports different back-ends, most importantly some (enhanced) suffix array implementations. Currently, there is no suffix array tool that works in all scenarios (for example whole genome, protein and RNA data). Bio::Grep provides a common API to the most popular tools. This way, you can easily switch or combine tools. Requirements: · Perl

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