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

Perl module sequence bl2seq sequence input/output stream bl2seq input/output

Bio::AlignIO::bl2seq Description

Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream.SYNOPSISDo 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();Requirements:· Perl

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