IMPALA: Matching a Protein Sequence Against a Collection of PSI-BLAST-constructed Position-Specific Score Matrices

Bioinformatics. 1999 Dec;15(12):1000-11. doi: 10.1093/bioinformatics/15.12.1000.


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.

MeSH terms

  • Algorithms
  • Bacterial Proteins / genetics
  • Databases, Factual*
  • False Negative Reactions
  • False Positive Reactions
  • Information Storage and Retrieval / methods*
  • Odds Ratio
  • Sequence Alignment
  • Sequence Analysis, Protein / methods*
  • Sequence Homology
  • Software*


  • Bacterial Proteins