title: Using the blocks database to recognize functional domains.
abstract: Blocks are ungapped multiple alignments of related protein sequence segments that correspond to the most conserved regions of the proteins. The Blocks Database is a collection of blocks representing known protein families that can be used to compare a protein or DNA sequence with documented families of proteins. Protocols in this unit describe the analysis of proteins and families using Blocks-based tools, including searching, exploring relationships with trees, making new blocks, and designing PCR primers from blocks for isolating homologous sequences.
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors.forename: Jorja G
authors.initials: JG
authors.lastname: Henikoff
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Greene
authors.forename: Nick
authors.initials: N
authors.lastname: Taylor
authors.forename: Steven
authors.initials: S
authors.lastname: Henikoff
authors.forename: Shmuel
authors.initials: S
authors.lastname: Pietrokovski
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D014584:User-Computer Interface