[Bioperl-l] 0.7 release: Blast

[Mark Dalphin]

> > What do we do -
> >
> >       - battle on with blast modules?
> >
> >       - fork bplite?
> >
> >       - rewrite?
>
> My humble suggestion is to wait a little longer until XML output becomes
> stable, and then write a new Blast parser which uses the DTD to parse the
> file and build the respective necessary data storage object(s).  Then
> deprecate the use of the old Blast parsing (I'd guess that those who use
> BioPerl for large scale blast parsing would also be able to control their
> blast output format option), in favor of XML-parsing.
>

We use wu-blast and I have not heard of whether there is any intent to switch to
XML output for that package. I would hate to see the Blast parser disappear
before both NCBI and wu-blast were ready with XML.

Mark

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Mark Dalphin                          email: mdalphin@amgen.com
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