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PubMed · 10870957

Blocks-based methods for detecting protein homology.

J G Henikoff·S Pietrokovski·C M McCallum·S Henikoff
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Abstract

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 NCBI's IMPALA programs, sequence logos, phylogenetic trees, three-dimensional display of blocks on PDB structures, and a polymerase chain reaction (PCR) primer design strategy based on blocks.

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Amino Acid SequenceAnimalsDNA PrimersDatabases, FactualHumansMolecular Sequence DataPolymerase Chain ReactionProteinsSequence Analysis, ProteinSequence Homology, Amino AcidJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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J G Henikoff, S Pietrokovski, C M McCallum, S Henikoff. 2000. Blocks-based methods for detecting protein homology.. https://doi.org/10.1002/(sici)1522-2683(20000501)21%3A9%3C1700%3A%3Aaid-elps1700%3E3.0.co%3B2-v

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