[pygr-notify] Issue 44 in pygr: tblastn and blastx support

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Comment #1 on issue 44 by cjlee112: tblastn and blastx support
http://code.google.com/p/pygr/issues/detail?id=44

Another possibility:
- since tblastn and blastx return protein-protein alignments, it might be  
more
intuitive for users to get back this protein-protein alignment.  One of the  
two
aligned protein sequences (dest for tblastn, and src for blastx) would be a
translation of the actual database sequence (nucleotide sequence).  We  
could model
this protein sequence as an annotation whose sequence attribute would  
correspond to
the nucleotide sequence interval that encodes it.

- This is pretty easy to implement, because the process_blast() method  
takes a
database argument for retrieving each sequence ID.  That database could be  
an
annotation db created specifically for translations.

- Question: how exactly to handle the coordinates returned by BLAST?   
Whereas it
returns a protein sequence, it gives nucleotide coordinates...  That  
implies a bit
more work.

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