[GUSDEV] blastSimilarity: broken coordinates when using TBLASTN

[Aaron J. M. <am...@pc...>]

FYI, the subject start/end coordinates of the SUM line seem to be  
fubar'ed in the short-form output (and the HSP lines are also  
suspect).  For instance:

   Sum: 995361:1777:2.1e-193:506993:506973:2:696:2:734:369:514:0:
    HSP1: 995361:336:463:645:1777:2.1e-193:508907:506973:2:639:0:
    HSP2: 995361:33:51:89:148:2.1e-193:506993:506727:610:696:0:

I believe this should instead look something like:

   Sum: 995361:1777:2.1e-193:506727:508907:2:696:2:734:369:514:1:
    HSP1: 995361:336:463:645:1777:2.1e-193:506973:508907:2:639:1:
    HSP2: 995361:33:51:89:148:2.1e-193:506727:506993:610:696:1:

I've only seen this in TBLASTN output, but there may be other  
algorithms that also behave poorly.

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
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