Wanted: Simple alignment software for education

Gustavo Glusman bmgustav at bioinfo.weizmann.ac.il
Sat Mar 9 16:18:23 EST 1996

In article <313DB38B.41C6 at mpiz-koeln.mpg.de> Jan T. Kim,
kim at mpiz-koeln.mpg.de writes:
>I am looking for alignment programs for educational purposes. The
>software should not be too sophisticated and loaded with features.
>Rather, we look for programs that produce an alignment out of two
>input sequences in a way which is as transparent to the user as
>possible, i.e. the scoring matrix should be made clear etc. It would
>be ideal if the program produced some sort of display of the process
>of constructing the path matrix, tracking the path etc.

Dear Jan,

Last year, a BioComputing course was held in BioMOO. (See my signature
for pointers to BioMOO, if you're not familiar with it). One of the
topics taught in this course was, naturally, pairwise alignment.
For this, I created an object in the MOO that lets you do more or less
what you ask for. It aligns sequences more or less interactively, showing
you the matrix, letting you decide how much of it to fill, etc.

For instructions, check:
(this file was written by Chris Perreault)

The MOO aligners are far from being perfect, but they are the closest
thing to what you asked for, that I know of. Let us know if you get any
better answers. :)

Best regards,

Gustavo Glusman               Founder/administrator of BioMOO
-- Gustavo at bioinformatics.weizmann.ac.il
-- http://bioinformatics.weizmann.ac.il/Gustavo
-- BioMOO: telnet bioinformatics.weizmann.ac.il 8888
           WWW:   http://bioinfo.weizmann.ac.il/BioMOO

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