[Bioperl-l] Bio::Tools::pSW stop codon bug?

[Chris Fields]

You should submit this as a bug via Bugzilla.  The first link gives  
some info on submitting bugs, the second is the actual Bugzilla link.

http://www.bioperl.org/wiki/Bugs

http://bugzilla.open-bio.org/

Make sure to create attachments for the script and data (no cut-and- 
paste).

I personally don't use pSW much, but we at least can test what's  
going on.  It may just be the way the local alignment behaves.  Maybe  
the algorithm doesn't like end gaps!

Chris

On Aug 8, 2006, at 7:18 PM, Prachi Shah wrote:

> Hi,
>
> I am trying to align very similar protein sequences with the
> Bio::Tools::pSW modules but running into an issue which seems like a
> bug. One of the two sequences is extended considerably with gaps so
> that an Amino acid residue matches the stop codon (*). I know there
> should not be any internal stop codons but we are working with a new
> assembly of the candida genome and we want to pick out such
> inconsistent cases. In any case, 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. Any help on
> this is appreciated.
>
> Thanks
> Prachi
>
>  Here is an example set of two sequences I am trying to align:
>
>> orf19.6264.3
> MSNYLNLAQFSGVTDRFNLERIKSDFSSVQSTISKLRPPQEFFDFRRLSKPANFGEIQQRVGYNLGYFSA 
> NYITIVLGLSIYALITNFLLLFVTIFVLGGIYGINKLNGEDLVLPVGRFNTSQLYTGLLIVAVPLGFLAS 
> PISTMMWLIGSSGVTVGAHAALMEKPIETVFEEEV*V
>> orf19.6264.3_old
> MSNYLNLAQFSGVTDRFNLERIKSDFSSVQSTISKLRPPQEFFDFRRLSKPANFGEIQQRVGYNLGYFSA 
> NYITIVLGLSIYALITNFLLLFVTIFVLGGIYGINKLNGEDLVLPVGRFNTSQLYTGLLIVAVPLGFLAS 
> PISTMMWLIGSSGVTVGAHAALMEKPIETVFEEEV
>
> 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' =>
> '/tools/perl/5.8.8/lib/site_perl/5.8.8/Bio/Ext/Align/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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign