Python Module for sequence alignments.

Alex cut_me_out at hotmail.com
Wed Jul 5 16:38:54 EST 2000



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

To use it on linux

tar zxf align.tgz
cd align
make

and make the align directory accessible to python, with a command like

setenv PYTHONPATH `pwd`:${PYTHONPATH}

It needs the Numeric extension.

Here's an example of how it works from the command line:

>>> import align                          
>>> align.align ('aneotuhaneot', 'asneouhoteuh')[0][0][:3]                
('neotuhane', 'sneouhote', '----uh--e')

The second element of the tuple it returns is the matrices used to
calculate the optimal alignments.

I don't really care how you use or change this, nor will I assume any
legal culpability for problems arising from its use.  For instance, if a
bug in this code tricks you into genetically engineering Giant
Super-Intelligent Man-Eating Lizards, I may cackle evilly, but I won't
explicitly own up.  I may take on the care and feeding of one or two of
them if you can prove they will co-exist peacefully with my cat, but
that's definitely as far as it goes.

But please do let me know of any problems with it, or any suggestions
you have about how I could improve it.  If you make any use or
improvements to it yourself, I would love to hear about them.

Alex.







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