Bio::Grep 0.10.6

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.


Product's homepage

Requirements:

· Perl