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Blocks-based methods for detecting protein homology

✍ Scribed by Jorja G. Henikoff; Shmuel Pietrokovski; Claire M. McCallum; Steven Henikoff

Publisher
John Wiley and Sons
Year
2000
Tongue
English
Weight
431 KB
Volume
21
Category
Article
ISSN
0173-0835

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✦ Synopsis

Blocks-based methods for detecting protein homology

The most highly conserved regions of proteins can be represented as blocks of aligned sequence segments, typically with multiple blocks for a given protein family. The Blocks Database World Wide Web (http://blocks.fhcrc.org) and e-mail (blocks@blocks. fhcrc.org) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments. We describe features for detection of distant relationships using blocks. Blocks+ includes protein families from the PROSITE, Prints, Pfam-A, ProDom and Domo databases. Other features include searching Blocks+ with the BLIMPS and NCBIΒ©s IMPALA programs, sequence logos, phylogenetic trees, threedimensional display of blocks on PDB structures, and a polymerase chain reaction (PCR) primer design strategy based on blocks.

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