[Bioperl-l] Bio::Tools::Run::RemoteBlast not getting all hits

[Dan Kortschak]

Hi All, I have been using Bio::Tools::Run::RemoteBlast to grab sequence
identities/species/etc for a largish set of coral EST to get an idea of
sequence conservation in the cnidarian lineage relative to vertebrates and
non-vertebrate bilaterians (insects and nematodes etc). After running the
script (largely based on Jason Stajich remote_blast example script - my
mess of it is pretty ugly so I haven't posted it) and manually validating
a proportion of the EST blast reports, I have found that a number of EST
failed to get blast matches and did not report a blast failure, but did
get matches when blasted manually. These failures were repeatable.
Does anyone have an idea what may be going on here.

thanks
Dan

I will post the script if necessary, but it's very ugly and kind of
embarassing, so I'd rather not.

I'm using bioperl 1.0 (debian wooby release).

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