Python implementation of BLAST alignment algorithm?

Question

Is anyone aware of a pure python implementation of BLAST alignment? I am trying to study this algorithm...

For those of us who aren't computational biologists: http://en.wikipedia.org/wiki/BLAST — Joe Kington, Aug 13 '10 at 18:19

score 3 · Answer 1 · answered Apr 28 '11 at 08:50

In fact a complete implementation of the BLAST algorithm is a quite hard. It has a lot of steps and optimizations. What could you do is: take a look of the BLAST Book from O'Reilly, for a very good explanation, take a look of the NCBI Blast code base, that it is big and hard to understand at the first glace, or, I sugest you to take a look at other BLAST implementation or may be, others algorithms like BLAT and Genoogle (http://genoogle.pih.bio.br/)

score -1 · Answer 2 · answered Aug 17 '10 at 06:34

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Try looking into BioPython:

http://biopython.org/

http://github.com/JoaoRodrigues/biopython/tree/GSOC2010

answered Aug 17 '10 at 06:34

poswald

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No, biopython does not implement Blast, it calls the canonical ncbi BLAST executable program that has to be installed independly – joaquin Feb 05 '12 at 14:13

Python implementation of BLAST alignment algorithm?

2 Answers2