[Biojava-dev] Alignment SmithWaterman and NW

[Emig, Robin]

	After tracking this down farther, I found the problem to be that
my sequences already had gaps in them before I did the alignment and the
tools in biojava treat gap, basically, like another symbol. Running the
same search on EMBOSS returns a correct result (water/needle) because it
removes/ignores gaps before doing the alignment.
Thanks,
robin 

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Sylvain
Foisy
Sent: Wednesday, November 08, 2006 5:03 PM
To: Emig, Robin
Cc: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] Alignment SmithWaterman and NW

Hi,

This might be a stupid question but have you tried these same sequences
using EMBOSS' water and needle with the same parameters? If you get the
same output, it might be the sequences themselves.

Best regards

Sylvain

On 08/11/06 17:27, "Emig, Robin" <Robin.Emig at pioneer.com> wrote:

> I just test out the alignment procedure in biojava and found a 
> possible issue. When aligning two sequences, I get an alignment which 
> contains gaps at the same position in both sequences. This seems 
> strange to me, can it be correct?


===================================================================

Sylvain Foisy, Ph. D.
Consultant
Diploide.net - TI pour la vie / IT for Life

Courriel: sylvain.foisy at diploide.net

===================================================================

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