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Bio::AlignIO::bl2seq(3pm) User Contributed Perl Documentation Bio::AlignIO::bl2seq(3pm)


Bio::AlignIO::bl2seq - bl2seq sequence input/output stream


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",
                             -report_type => "blastn");
    $aln = $in->next_aln();


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

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

   # Get two 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);
   # Note that report is a Bio::SearchIO object
   # Use to create a SimpleAlign object from the bl2seq report
   $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
   $aln = $str->next_aln();


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Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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AUTHOR - Peter Schattner



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $alignio = Bio::SimpleAlign->new(-format => 'bl2seq',
                                               -file   => 'filename',
                                               -report_type => 'blastx');
 Function: Get a L<Bio::SimpleAlign>
 Returns : L<Bio::SimpleAlign> object
 Args    : -report_type => report type (blastn,blastx,tblastx,tblastn,blastp)


 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : L<Bio::Align::AlignI> object on success,
           undef on error or end of file
 Args    : none


 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in bl2seq format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object


 Title   : report_type
 Usage   : $obj->report_type($newval)
 Function: Sets the report type (blastn, blastp...)
 Returns : value of report_type (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
2021-08-15 perl v5.32.1