[Bioperl-guts-l] [Bug 2069] New: Bio::Tools:pSW stop codon bug

[bugzilla-daemon at newportal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2069

           Summary: Bio::Tools:pSW stop codon bug
           Product: Bioperl
           Version: main-trunk
          Platform: Other
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P2
         Component: bioperl-ext
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: prachi at stanford.edu


I am trying to align very similar protein sequences with the
Bio::Tools::pSW modules but running into a bug. One of the two sequences is
extended with gaps so that an Amino acid residue matches the stop codon (*).
The alignment should match the two sequences (because they are the same) up
until the stop codon is encountered in the new sequence. Instead, it
artificially extends the old sequence and matches the Alanine with the stop
codon. 


 Here is an example set of two sequences I am trying to align:

>orf19.6264.3
MSNYLNLAQFSGVTDRFNLERIKSDFSSVQSTISKLRPPQEFFDFRRLSKPANFGEIQQRVGYNLGYFSANYITIVLGLSIYALITNFLLLFVTIFVLGGIYGINKLNGEDLVLPVGRFNTSQLYTGLLIVAVPLGFLASPISTMMWLIGSSGVTVGAHAALMEKPIETVFEEEV*V
>orf19.6264.3_old
MSNYLNLAQFSGVTDRFNLERIKSDFSSVQSTISKLRPPQEFFDFRRLSKPANFGEIQQRVGYNLGYFSANYITIVLGLSIYALITNFLLLFVTIFVLGGIYGINKLNGEDLVLPVGRFNTSQLYTGLLIVAVPLGFLASPISTMMWLIGSSGVTVGAHAALMEKPIETVFEEEV

and below is the part of code that generates the alignments --

################
my $new_translatedSeqObj = Bio::Seq->new(-display_id => $gene,
                                                                    -seq       
=> $new_translatedSeq);

my $old_translatedSeqObj = Bio::Seq->new(-display_id => $gene. "_old",
                                                                    -seq       
=> $old_translatedSeq);

# do alignments
my $align_factory = new Bio::Tools::pSW( '-matrix' =>'blosum62.bla',
                                         '-gap' => 12,
                                         '-ext' => 2 );

my $aln = $align_factory->pairwise_alignment( $old_translatedSeqObj,
$new_translatedSeqObj );

my $alnout = new Bio::AlignIO(-format => 'clustalw',
                              -fh     => \*STDOUT);

##################

The alignment --

CLUSTAL W(1.81) multiple sequence alignment


orf19.6264.3_old/1-162
MSNYLNLAQFSGVTDRFNLERIKSDFSSVQSTISKLRPPQEFFDFRRLSKPANFGEIQQR
orf19.6264.3/1-177
MSNYLNLAQFSGVTDRFNLERIKSDFSSVQSTISKLRPPQEFFDFRRLSKPANFGEIQQR

************************************************************


orf19.6264.3_old/1-162
VGYNLGYFSANYITIVLGLSIYALITNFLLLFVTIFVLGGIYGINKLNGEDLVLPVGRFN
orf19.6264.3/1-177
VGYNLGYFSANYITIVLGLSIYALITNFLLLFVTIFVLGGIYGINKLNGEDLVLPVGRFN

************************************************************


orf19.6264.3_old/1-162
TSQLYTGLLIVAVPLGFLASPISTMMWLIGSSGVTVGAHA---------------AL
orf19.6264.3/1-177    
TSQLYTGLLIVAVPLGFLASPISTMMWLIGSSGVTVGAHAALMEKPIETVFEEEV*V
                      ****************************************                :


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