PURPOSE This protocol is intended to be run using output files from a BLAST or PSI-BLAST job.
To run this protocol, the user must specify the BLAST or PSI-BLAST output .xml and .pir files as well as the database used to generate this data.
The Output folder will contain a new version of the .pir file in which the sequence name for each sequence will have the organism name appended to it (if such a name is provided in the input .xml file).
Organism information appears to be available when BLAST is run against the PDB_nr95, nr and pdbaa databases.
Note, if there are other databases in which this information is available, the protocol may be modified to include those as well.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio only, go to the Protocol Explorer, right-click over the folder you want to add the protocol to, choose Import, navigate to the location of the Add Organism Name to Pir (from BLAST).xml file and enter it as the File Name.

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.0 and 2.1 and Pipeline Pilot 6.1.5 and 6.1.6. It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.