The rpsbproc command line utility is an addition to the standalone version of Reverse Position-Specific BLAST (RPS-BLAST), also known as CD-Search (Conserved Domain Search).

It post-processes the results of local RPS-BLAST searches in order to provide a non-redundant view of the search results, and to provide additional annotation on query sequences, such as domain superfamilies and functional sites, similar to the annotation provided by the corresponding web services (e.g., the NCBI Batch CD-Search web service at http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi).

Specifically, the rpsbproc utility reads the output of rpsblast/rpstblastn, fills in domain superfamily and functional site information for each region of the sequence, re-sorts the hits by a different standard, and calculates a set of non-redundent representative hits. In this way, it turns the raw alignments into domain/site annotations on the query sequence at different redundancy level, basically produce the same data as web-based Batch CD-Search service does. The annotation data is presented in tab-delimited tables to be processed either programatically or manually with a spreadsheet (see details below).

See the CDD and CD-Search help document for additional details about superfamilies, conserved sites, and more:

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml