[Biojava-dev] Alignment SmithWaterman and NW
Robin.Emig at pioneer.com
Fri Nov 10 21:00:43 EST 2006
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.
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Sylvain
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
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.
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.
Diploide.net - TI pour la vie / IT for Life
Courriel: sylvain.foisy at diploide.net
biojava-dev mailing list
biojava-dev at lists.open-bio.org
This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
use of sender's contact information for direct marketing purposes or for
transfers of data to third parties.
Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean
More information about the biojava-dev