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PMID: 9399861 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Superior performance in protein homology detection with the Blocks Database servers.

Nucleic acids research ·Vol. 26 ·No. 1 ·1998-01-01 ·Pages 309-12

Henikoff S, Pietrokovski S, Henikoff JG

Abstract

The Blocks Database World Wide Web (http://www.blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org) servers provide tools for the detection and analysis of protein homology based on alignment blocks representing conserved regions of proteins. During the past year, searching has been augmented by supplementation of the Blocks Database with blocks from the Prints Database, for a total of 4754 blocks from 1163 families. Blocks from both the Blocks and Prints Databases and blocks that are constructed from sequences submitted to Block Maker can be used for blocks-versus-blocks searching of these databases with LAMA, and for viewing logos and bootstrap trees. Sensitive searches of up-to-date protein sequence databanks are carried out via direct links to the MAST server using position-specific scoring matrices and to the BLAST and PSI-BLAST servers using consensus-embedded sequence queries. Utilizing the trypsin family to evaluate performance, we illustrate the superiority of blocks-based tools over expert pairwise searching or Hidden Markov Models.

MeSH Terms
Amino Acid Sequence Animals Computer Communication Networks Conserved Sequence Databases, Factual Humans Proteins/chemistry Sequence Homology, Amino Acid
Chemicals
Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Henikoff S
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. steveh@muller.fhcrc.org
Pietrokovski S
Henikoff J G
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/26.1.309
Email
steveh@muller.fhcrc.org
Published
1998-01-01
Pages
309-12
Language
English
Region
England
NLM ID
0411011
PMCID
PMC147168
Subset
IM
Grants
NIGMS NIH HHS · GM29009 · United States
External Links
PubMed source DOI: 10.1093/nar/26.1.309 PMC Full Text View journal details
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