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.
I've got a radical suggestion for you.
We're teaching a computational biology course at Washington
University, and we've run across the same problem -- how to get people
to understand dynamic programming. We tried to do it the hard way by
asking people to do some small DP matrices by hand. Tedious as hell.
A grad student in my group managed to automate the whole thing for
himself in an Excel spreadsheet with a small amount of work. His
spreadsheet became a DP matrix, automatically updating when you change
a sequence position or your scoring system (he used a simple scoring
matrix for identities/mismatches). It doesn't do the traceback,
If you have any Excel-savvy folks around, you might consider
this. It's a hack but it's quick, easy, and informative.
- Sean Eddy
- Dept. of Genetics, Washington University School of Medicine
- eddy at genetics.wustl.edu