[Bioperl-l] Problem parsing clustalw format ni AlignIO

[Catherine Letondal]

Hi bioperlers,

I have a script called protal2dna 
(http://bioweb.pasteur.fr/seqanal/interfaces/protal2dna.html, see 
attachment #1) that realign DNA sequences giving their sequences + the 
corresponding protein alignment (sequences have to be in the same order 
or named equivalently). We have a parsing problem reported from the 
AlignIO class when users enter some clustalw file (see attachment #2 
for an example):

% protal2dna alig-protal2dna.dat dna-protal2dna.data
no alignment available in 'clustalw' format from file 
'alig-protal2dna.dat'
%

I have tried with bioperl 1.4. I have looked in the archive and in the 
BUGS, but found nothing?
Is there any bug fix for this? I also provide the DNA sequences file if 
you want to test.

Thanks a lot in advance,

--
Catherine Letondal -- Institut Pasteur
www.pasteur.fr/~letondal

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