Bioperl: Module collections...

Steven E. Brenner
Sat, 1 Aug 1998 16:03:31 +0100

> > Looking ahead to next week when chris and I are going to 
> > get together to make the CVS system I'm downloading modules
> > to put in....
> > 
> > a) (can we start calling this now?)
> The name change should coincide with a functionality change, namely, 
> adding a feature description mechanism. We'll have to hear from ChrisD 
> and Ian about their progress along these lines.

  I think we should think very carefully about the interfaces to, and I don't know that PreSeq is tested well enough for us to
be certain that we are happy with the interfaces.    Once we create, I hope that its interfaces will remain fairly constant.

  Therefore, I think it is best to keep developing for some

Regarding BLAST,

   there are a fair number of modules around, and I should also note that
I believe that a new, parsable output format will be released by NCBI
before tooooo long.  We also will want to incorporate the ability to pass
more flags to control PSI-BLAST. Furthermore, I think it is helpful to
have the 'running' and the 'parsing' modules separate (with perhaps some
wrapper module which does both).  So, I think it is premature to do too
much with these modules.


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