[bip] developing tutorials, code samples, etc.

Titus Brown titus at caltech.edu
Thu Sep 20 16:23:58 PDT 2007


On Wed, Sep 19, 2007 at 08:39:52PM -0300, Sebastian Bassi wrote:
-> On 9/19/07, Brandon King <kingb at caltech.edu> wrote:
-> > >  - a "blastparser" tutorial describing how to parse basic BLAST reports
-> > >    and then calculate reciprocal BLAST matches;
-> > >
-> > I think the "blastparser" tutorial would likely be useful to many
-> > people, so I would vote for this one.
-> 
-> I could work on a blastparser tutorial, but I don't know what it's
-> means with "reciprocal BLAST matches".

Hi, Sebastian,

reciprocal best match or reciprocal match are (quick and diry) ways of
calculating putative orthologs and homologs, respectively.

If you have genes A and A' from genomes G and G', A and A' are
considered orthologs if A' is the best match to A in genome G',
and A is the best match to A' in the genome G.

Were BLAST a symmetric search algorithm, A => A' would always imply A'
=> A; as it is not symmetric, you need to do the BLASTs both ways.

I'm curious -- what BLAST parser are you using? BioPython's?  Your own?
mine?

cheers,
--titus



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