Paper Info
Title
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
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.
Year
DOI
Venue
1999
10.1093/bioinformatics/15.12.1000
BIOINFORMATICS
Keywords
Field
DocType
local alignment,protein folding,database search,statistical significance,source code,signal transduction,protein domains,protein sequence
Sequence alignment,Data mining,File Transfer Protocol,Protein sequencing,Source code,Computer science,Unix,Software,Smith–Waterman algorithm,Bioinformatics,Executable
Journal
Volume
Issue
ISSN
15
12
1367-4803
Citations 
PageRank 
References 
76
12.39
17
Authors
6
Name
Order
Citations
PageRank
Alejandro A. Schäffer1827136.66
Yuri I. Wolf254076.15
Chris P. Ponting3733283.28
Eugene V. Koonin4986239.69
L. Aravind510916.49
Stephen F Altschul618026.55