[Bioperl-l] Bio::Tools::Blast and BPLite

[Wiepert, Mathieu]

Regarding the Blast modules...Is there still an interest to
have a heavyweight Blast parser such as Bio::Tools::Blast, or  will BPLite
suffice for all Blast parsing/running needs?

I guess I can't say which is better, but it seems that whatever is getting
more support is better.  I can selfishly say that I want to be able to parse
different types of blast output:  the default blast output and the
query-anchored showing identities (view=1 in GCG anyway).  I have achieved
that (finally) without bioperl, but I bet it can be much better if I use it
WITH bioperl, extending the current functionality here already.  That's the
next task for me ;-)

One thing that I would like to better understand is the GAME dtd, and all
the info that it can represent.  If it can represent the data from all the
blast outputs, and you can just populate it with the bits you glean from
each one, then that would be good.  You can parse any type of blast output
to XML, and transform to whatever you need.

Lastly, I am not clear on the relative advantages and disadvantages of the
heavy vs. lite parsers, though being able to have it both ways would be good
of course.  Any opinions on that?  Anyway, that's my limited 2 cents from a
new user, take it for what it's worth!

 - Mat