title: Blocks-based methods for detecting protein homology.
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.
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. steveh@fhcrc.org
authors.forename: J G
authors.initials: JG
authors.lastname: Henikoff
authors.forename: S
authors.initials: S
authors.lastname: Pietrokovski
authors.forename: C M
authors.initials: CM
authors.lastname: McCallum
authors.forename: S
authors.initials: S
authors.lastname: Henikoff
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017931:DNA Primers; D016208:Databases, Factual; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D011506:Proteins / Q000032:analysis*; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid
chemical_list: D017931:DNA Primers; D011506:Proteins