Python implementation of BLAST alignment algorithm?

Question

Does anyone know of a pure python implementation of BLAST alignment? I am trying to learn this algorithm ...

Answer 1

In fact, the full implementation of the BLAST algorithm is rather complicated. It has many steps and optimizations. What you can do: take a look at O'Reilly’s BLAST book, for a very good explanation, look at the NCBI Blast code base that it is very large and hard to understand at a glance, or, sugest you take a look at another BLAST implementation or maybe , other algorithms such as BLAT and Genoogle (http://genoogle.pih.bio.br/)

Answer 2

Try exploring BioPython:

http://biopython.org/

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