[Bioperl-l] Remote BLAST support discussion

Roger Hall rahall2 at ualr.edu
Fri Feb 10 17:54:23 UTC 2006

It seems so obvious now. :}

The only issue I see is likely obvious to those of you who have maintained
this over the years - no backward compatibility, but I can live with that if
yall can.

I will document on wikki as suggested and then build the RemoteNCBI module
described. After that is tested and committed, I will contact Torsten to see
if I can help with the rest.



> Bio::Tools::Run::Blast
>   -->             StandAlone (support for both WU-BLAST and NCBI-> BLAST
local binaries and MPI-BLAST too if simple)
>   -->             RemoteNCBI (currently the RemoteBlast server)
>   -->             RemoteEBISOAP (EBI has a nice SOAP interface that works
quite well, but may not provide all the same databases as what people expect
from NCBI)
>   -->             RemoteNetBlast (blastcl3 or netblast local executable)
>   (other things that people want)

Sounds good to me.  I think any wrapper for netblast could most easily be
based on StandAloneBlast; the parameters look pretty much identical, though
it'll probably need a little configuring as a quick text search through
StandAloneBlast didn't show any 'xml' tags.  Roger seemed to agree on this.

More information about the Bioperl-l mailing list