Python Module for sequence alignments.

Ognen Duzlevski ogd116 at duke.usask.ca
Mon Jul 10 17:58:20 EST 2000


Hello,

I have played with the dynamic programming algorithm for obtaining
sequence alignments -> beta-beta-beta code is at
http://www.cs.usask.ca/undergrads/ogd116/seqalign/

I toyed with the idea of parallelizing the whole dynamic programming
algorithm - further more, writing as bunch of parallelized agents sitting
around on a local network and crunching on the same sequence database - I
believe (hope) this would speed up things greatly.

I used the dynamic programming algorithm explained
at: http://www.cs.washington.edu/education/courses/527/00wi/lectures/lect04.pdf

Best regards,
Ognen Duzlevski

On 7 Jul 2000, Andrew Dalke wrote:

: Alex wrote:
: >Hi.  I made a python module that does simple sequence alignments.  If
: >there is enough interest, I may make it a little more elaborate.  You
: >can get it from
: >
: >http://puffin.lcs.mit.edu:8080/align.tgz
: 
: By the way, you may be interested in biopython.org, which is developing
: a set of libraries and tools for bioinformatics and related fields.  You
: may also be interested in the Bioinformatics Open-Source Conference
: <ismb2000.sdsc.edu/bosc2000> which really should include your
: disclaimer concerning Giant Super-Intelligent Man-Eating Lizards.
: 
:                     Andrew
:                     dalke at acm.org

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