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PMID: 9705509 Published · ppublish English Comparative Study Journal Article

Protein sequence similarity searches using patterns as seeds.

Nucleic acids research ·Vol. 26 ·No. 17 ·1998-09-01 ·Pages 3986-90

Zhang Z, Schäffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF

Abstract

Protein families often are characterized by conserved sequence patterns or motifs. A researcher frequently wishes to evaluate the significance of a specific pattern within a protein, or to exploit knowledge of known motifs to aid the recognition of greatly diverged but homologous family members. To assist in these efforts, the pattern-hit initiated BLAST (PHI-BLAST) program described here takes as input both a protein sequence and a pattern of interest that it contains. PHI-BLAST searches a protein database for other instances of the input pattern, and uses those found as seeds for the construction of local alignments to the query sequence. The random distribution of PHI-BLAST alignment scores is studied analytically and empirically. In many instances, the program is able to detect statistically significant similarity between homologous proteins that are not recognizably related using traditional single-pass database search methods. PHI-BLAST is applied to the analysis of CED4-like cell death regulators, HS90-type ATPase domains, archaeal tRNA nucleotidyltransferases and archaeal homologs of DnaG-type DNA primases.

MeSH Terms
Adenosine Triphosphatases Algorithms Amino Acid Sequence Archaeal Proteins Caenorhabditis elegans Proteins Calcium-Binding Proteins DNA Primase Databases, Factual HSP90 Heat-Shock Proteins Helminth Proteins Pattern Recognition, Automated RNA Nucleotidyltransferases Software
Chemicals
Archaeal Proteins Caenorhabditis elegans Proteins Calcium-Binding Proteins Ced-4 protein, C elegans HSP90 Heat-Shock Proteins Helminth Proteins DNA Primase RNA Nucleotidyltransferases Adenosine Triphosphatases
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Zhang Z
Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
Schäffer A A
Miller W
Madden T L
Lipman D J
Koonin E V
Altschul S F
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/26.17.3986
Published
1998-09-01
Pages
3986-90
Language
English
Region
England
NLM ID
0411011
PMCID
PMC147803
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/26.17.3986 PMC Full Text View journal details
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