Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | 1000-11 |
| Number of pages | 12 |
| Journal | Bioinformatics |
| Volume | 15 |
| Issue number | 12 |
| Publication status | Published - Dec 1999 |
Keywords
- Algorithms
- Bacterial Proteins
- Databases, Factual
- False Negative Reactions
- False Positive Reactions
- Information Storage and Retrieval
- Odds Ratio
- Sequence Alignment
- Sequence Analysis, Protein
- Sequence Homology
- Software