[Biopython-dev] SearchIO HSP indexing

[Wibowo Arindrarto]

Hi everyone,

Colin, thanks for the feedback! Peter has explained the rationale
behind the decision, so I would like to add that there has been indeed
an explanation of this behavior in the tutorial
(http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc106) and
the code (https://github.com/biopython/biopython/blob/master/Bio/SearchIO/__init__.py#L100).
I do admit that the explanation in the code could be made clearer with
some comments in hsp.py ~ which I can add :).

As for your point about the alignment code:

> I was wondering if there was any code in SearchIO to align high-scoring
> segment pairs against the same hit? I see the fragmentation code but that
> seems specific to BLAT results and when I look at the HSPFragments in the
> QueryResult object it does not seem to combine multiple HSPs against the
> same hit even if they are not overlapping.

SearchIO relies on BLAST to do this ~ which has already grouped each
HSP aligning to the same database sequence in one group (all of which
is accessible through the Hit object). I've always assumed that if two
HSPs came from the same database entry (Hit), they are grouped into
one Hit by BLAST, regardless of whether they overlap or not. Have you
seen any results from BLAST that shows otherwise?

cheers,
Bow