Bio::AlignIO::bl2seq 1.4

Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream.

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class, as in:

use Bio::AlignIO;

$in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq);
$aln = $in->next_aln();

This object can create Bio::SimpleAlign sequence alignment objects (of 2 sequences) from bl2seq BLAST reports.

A nice feature of this module is that- in combination with StandAloneBlast.pm or remote blasting - it can be used to align 2 sequences and make a SimpleAlign object from them which can then be manipulated using any SimpleAlign.pm methods, eg:

#Get 2 sequences
$str = Bio::SeqIO->new(-file=>t/amino.fa , -format => Fasta, );
my $seq3 = $str->next_seq();
my $seq4 = $str->next_seq();

# Run bl2seq on them
$factory = Bio::Tools::StandAloneBlast->new(program => blastp,
outfile => bl2seq.out);
my $bl2seq_report = $factory->bl2seq($seq3, $seq4);

# Use AlignIO.pm to create a SimpleAlign object from the bl2seq report
$str = Bio::AlignIO->new(-file=> bl2seq.out,-format => bl2seq);
$aln = $str->next_aln();