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