'Reversed Position Specific BLAST', or RPS BLAST, is a very fast alternative to the program IMPALA. It has the same general objective, e.g, to compare a sequence to a collection of conserved domains (aka motifs, profiles, HMMs, position specific matrices, or PSSM). The RPS BLAST program has a completely different implementation. Through database indexing, it has increased the speed of profiles search 10 to 100 times (depending on search conditions) in comparison to IMPALA. RPS BLAST has an option to perform translated searches of DNA sequences against these conserved domains. RPS BLAST is the basis for the CDD search page.
There is a small RPS database available for testing under the /db/CDD/ directory with a few entries from the real NCBI database used in CDD search page. The complete NCBI cdd database is available in preformatted format from: ftp://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/.
Databases for RPS BLAST are hardware dependent for speed reasons. Hence they are different for big vs little endian platforms. Users need to make sure they get the correct database for their platforms. To build RPS database, it is necessary to follow the procedure explained in the file formatrpsdb.html. An end user oriented document on formatrpsdb is at: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatrpsdb.html.