[Biopython-dev] [Bug 1715] New: Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Dec 6 16:44:59 EST 2004


           Summary: Bio.Blast.NCBIStandalone does not support standalone
                    NCBI RPS-Blast (rpsblast) output
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk

The NCBI's standalone RPS-Blast program (Reverse Position Specific BLAST) can be
used to query a protein sequence against the Conserved Domain Database, or Pfam,
or SMART etc.

The commandline program rpsblast(.exe) is very similar in use to the existing
blastall(.exe), and the resulting output file simply seems to omit some lines.

I have been able to modify the NCBIStandalone.py as shipped with BioPython 1.30
to support rpsblast as well.  Attachments to follow.

See also this email and any follow ups:


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