title: IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
abstract: BACKGROUND
  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.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. schaffer@helix.nih.gov
authors.forename: A A
authors.initials: AA
authors.lastname: Schäffer
authors.forename: Y I
authors.initials: YI
authors.lastname: Wolf
authors.forename: C P
authors.initials: CP
authors.lastname: Ponting
authors.forename: E V
authors.initials: EV
authors.lastname: Koonin
authors.forename: L
authors.initials: L
authors.lastname: Aravind
authors.forename: S F
authors.initials: SF
authors.lastname: Altschul
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics; D016208:Databases, Factual; D005188:False Negative Reactions; D005189:False Positive Reactions; D016247:Information Storage and Retrieval / Q000379:methods*; D016017:Odds Ratio; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D017385:Sequence Homology; D012984:Software
chemical_list: D001426:Bacterial Proteins