[Bioperl-l] AlignIO problems

Chris Fields cjfields at uiuc.edu
Mon Feb 26 12:18:38 EST 2007

On Feb 26, 2007, at 9:59 AM, 江 文恺 wrote:

> Thank you!
> I have checked the sequences retrieved through lots of Bio:DB  
> objects work simultaneously.
> There are not problems you mentioned, the sequences are not  
> overwritten.

Again, keep this on the list.  I have my hands full this month so I  
will be checking the list only very sporadically; someone else may be  
able to help you.

The only explanation for the clustalw output you get is that you are  
not retrieving the correct sequence in some way fundamental way,  
which to me indicates the bug originates either in the way the  
sequences are retrieved (i.e. somehow via Bio::DB::Fasta, hence my  
thought about conflicting indices) or in the way they are converted  
via Bio::SeqIO, which is used in Bio::Tools::Run::Alignment::Clustalw.

When I have used Bio::DB::Fasta in the past I have never had a  
problem when indexing multiple files and retrieving sequences, so  
beyond running tests with your data I can't help you much beyond the  
above conjecturing.


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