[Bioperl-l] RPSblast and existing BLAST packages (WAS: RemoteBlast)

[Donald G. Jackson]

Paul and Richard and the rest of bioperl-l,

as I volunteered to maintain StandAloneBlast.pm, I've been thinking 
about including RPSblast since the topic came up on the list a few days 
back.   I can see the argument for doing this - since RPSblast is part 
of the NCBI blast kit - but conceptually I think of RPSblast as more 
similar to HMMsearch and such, and a lot of how I'd access the results 
is also similar.

Above all, RemoteBlast and StandAloneBlast should be consistent - I like 
the idea of a BlastI standard .  I wonder if we should be supporting all 
the Blast programs in a monolithic package or breaking them out more, at 
least wrt new capabilities like RPSblast.  What are your thoughts?

Don Jackson