[Bioperl-l] ClustaW error

[Heikki Lehvaslaiho]

There is an error in ClustalW code that adds a character to the end of
some aligned sequences during profile alignment. I reported it to
ClustalW developers and here is the fix for CLustalW version 1.81
(latest):

> The changes need to be made in lines 184-185 and 216-217 of prfalign.c. 
> The new lines are:
> 
> 184-185:
>                         alignment[nseqs1][j]=gap_pos1;
>              alignment[nseqs1][j] = ENDALN;
> 216-217:
>                         alignment[nseqs1+nseqs2][j]=gap_pos1;
>              alignment[nseqs1+nseqs2][j] = ENDALN;
> 

The same bug is likely to be in older versions, too, but I have not
checked.

The bug is detected by new code in Bio::LocatableSeq::end which prints
a warning. Tests 8 and 9 in t/Clustalw.t fail because of this, too.
The error is also present in branch-07, but goes undetected.

I've  committed changes to t/Clustalw.t error messages. In my opinion,
once the fixed version of ClustalW is out, it is time to implement a
system that checks external program versions. 

	-Heikki "For once I spell checked my message!"



-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________