Bioinformatics Vol. 15 no. 12 1999
Pages 1000-1011
© 1999 Oxford University Press
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
1 National Center for Biotechnology
Information, National Library of Medicine, National Institutes of
Health, Bethesda, MD 20894, USA
2 Department of Biology, Texas A&M
University, Biological Sciences Building West, College Station, TX
77843, USA
Present address: MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK.
Motivation: Many studies have shown that database searches using position-specific score matrices (PSSMs) or profiles as queries are more effective at identifying distant protein relationships than are searches that use simple sequences as queries. One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST).
Results: This paper describes a new software package, IMPALA, designed for the complementary procedure of comparing a single query sequence with a database of PSI-BLAST-generated PSSMs. We illustrate the use of IMPALA to search a database of PSSMs for protein folds, and one for protein domains involved in signal transduction. IMPALA’s sensitivity to distant biological relationships is very similar to that of PSI-BLAST. However, IMPALA employs a more refined analysis of statistical significance and, unlike PSI-BLAST, guarantees the output of the optimal local alignment by using the rigorous Smith–Waterman algorithm. Also, it is considerably faster when run with a large database of PSSMs than is BLAST or PSI-BLAST when run against the complete non-redundant protein database.
Availability: The IMPALA source code, the wolf1187 database, and the aravind105 database are freely available from the NCBI ftp site ncbi.nlm.nih.gov. The databases may be found in the subdirectory ftp://ncbi.nlm.nih.gov/pub/impala. The source code is in ftp://ncbi.nlm.nih.gov/toolbox/ncbi·tools. Some IMPALA executables for different implementations of UNIX are in ftp://ncbi.nlm.nih.gov/blast/executables. IMPALA has been added as a search option on the Blocks Database Server (http://blocks.fhcrc.org/blocks/impala.html)using a library of PSSMs derived from the BLOCKS database.
Contact: schaffer{at}helix.nih.gov
Received on March 19, 1999
; revised on July 28, 1999
; accepted on August 4, 1999
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