[Bioperl-l] 0.7 release: Blast

Hilmar Lapp hlapp@gmx.net
Tue, 14 Nov 2000 09:04:34 -0800

Ewan Birney wrote:
> code. However, I don't think we will be able to tease out the Root::Object
> >from the blast code, and we can't remove the code (backward compatibility)
> even though we have BPLite in.

Just to mention, the Blast module offers also more functionality than
BPlite (which is probably intentional, as the name BPlite implies). I'm
for instance using the frac_identical() (_conserved etc) methods
exploiting the tiling of HSPs, which is what you need if you want to
know how much of your query sequence is matched by the subject (and vice

So, I personally don't want to let people get the impression that in
fact we want to abandon Blast.pm sooner or later. Maintenance of that
module is, however, obviously a problem, as SteveC seems to be too busy
with other things, and it is too complicated for someone else of the
developers to jump in.

The question is whether as a consequence Blast.pm will have to be
abandoned at some time though (contradicting myself :) In this case I
think it is essential to migrate some of the important functionality of
Blast.pm that makes its difference to Ian Korf's code. Again, this is
not so simple in a 'logistic' sense, because BPlite in BioPerl is only a
ported version (how much does it differ from the original version?

When I noticed that this is sort of off topic, I changed the subject
line; it's probably not even something we can or should address for the
0.7 release.

What do people think?


Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757