[BioPython] Clustalw multiple alignment

[Jeffrey Chang]

Scripting code that provides interfaces to programs are certainly needed
within biopython!  Should we include this package in the distribution?

This seems to have a lot of requirements that currently aren't in the
Biopython spec (Python 1.6+, XML, Martel), but perhaps that means it's
time to update the requirements list.

Jeff



On 23 Sep 2000, Brad Chapman wrote:

> Hello all;
> 	I have been doing some work where I wanted to be able to interact
> with the clustalw multiple alignment program. Basically, what I wanted to
> do was to be able to set up a command line for clustalw, run clustalw,
> parse the results and manipulate these result, all from within python.
> 
> So I wrote up some code which does the following stuff:
> 
> 1. Provides a class to model the clustalw command line so that you can
> set parameters you want from python.
> 
> 2. Parses clustal formatted files (with *.aln extensions) using Martel
> (Andrew's latest version) into a class which holds the sequences as
> SeqRecord objects, and can write the alignment back out in the clustal
> format.
> 
> 3. Has some convenience functions to run clustal and parse the results
> all in one shot.
> 
> 4. Does a quick calculation of a consensus sequence from a bunch of
> aligned objects.
> 
> I put the code for this at:
> 
> http://www.bioinformatics.org/bradstuff/bp/align.tar.gz
> 
> I was wondering if people had time to take a look at this and give me
> feedback on it. I would like to also do something similar for pairwise
> alignment code (any suggestions for existing C code to use?) so that I
> could quickly compare two sequences and get an alignment score between
> them.
> 
> The kind of feedback I am interested in is:
> 
> 1. Is this kind of code useful to anyone besides me?
> 
> 2. Do the interfaces make sense? How can they be improved?
> 
> 3. Do you see any bugs, etc?
> 
> Thanks for listening, and enjoy!
> 
> Brad
> 
> 
> 
> 
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