[Bioperl-l] RemoteBlast

[Torsten Seemann]

Roger,

> I think that most core Bioperl folks have long since moved away from
> RemoteBlast and are using the functionality in StandAloneBlast to run their
> own local servers. 

Agreed. Even smaller centres like my workplace need the throughput that
a local PC, SMP system or Cluster can provide.

> wave of the future, but I think there is still some concern that not every
> flavor of BLAST produces XML yet. Even so, the XML parser is considered to
> be very strong, and only helps hasten the end of text-formatted support,
> since parsing text-formatted reports is the primary source of pain. 

If BioPerl switches primarily to XML parsing, the tool authors will soon
add support for XML (not very difficult really) due to BioPerl's
pervasiveness?

> I do, however, see the advantage in shifting to XML-formatted reporting and
> parsing *only* as soon as every BLAST flavor supports it, if not before.
> (Anyone - is this still an issue. Please educate me.)

The four BLAST flavours I utilise all support XML output: 
1) NCBI BLAST 2) WU-BLAST 3) MPI-BLAST 4) FSA-BLAST.

> At the moment, I'm leaning towards adding an option to RemoteBlast. The
> default (no option) would use a "pure perl" implementation, and the
> enhancement (with explicit option) would merely wrap the NCBI executable.

If the API is done correctly both of these could co-exist with very
little redundant code. (I personally rarely use remote blast).

-- 
Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
Victorian Bioinformatics Consortium