Database BLOCKS

S Pietrokovski, JG Hemkoff, S Henikoff. The BLOCKS database—A system for protein classification. Nucleic Acids Res 24 197-200, 1996. 

JG Henikoff, S Henikoff. BLOCKS database and its applications. Methods Enzymol 266 88-105, 1996. 

The BLOCKS database contains blocks for each family (Henikoff and Henikoff, 1991 Henikoff et al., 1999). Blocks are ungapped multiple sequence alignments that are exacdy equivalent to the motifs found in the PRINTS database. The families in BLOCKS are currently derived from Prosite and PRINTS families. The bulk of BLOCKS entries are constructed from Prosite, using the lists of true positive members they provide. Motifs are automatically derived from the members of the Prosite family. Note that BLOCKS does not use the Prosite patterns to construct its motifs. BLOCKS provides functionality to search motifs against motifs this feature is not provided by other databases. 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

To search amino acid sequence against the BLOCKS database at http // www.blocks.fhcrc.org/, select Block Searcher to open the search form. Choose the options, paste the query sequence, and click the Perform Search button. The search returns lists of matched blocks (I.D. descriptions, number of blocks, and combined E values), locations (amino acid positions of individual blocks and its E value), and pairwise alignment of the blocks with the matched query sequences (Figure 12.17). 

Figure 12.17. Search a sequence against Blocks database. The search of cod alcohol dehydrogenase sequence against Blocks database returns a list of hits and pairwise alignments of blocks (only one set is shown).

Henikoff, J. G., Henikoff, S. Pietrokovski, S. (1999). New features of the Blocks Database servers. Nucleic Acids Res 27,226-8. 

The BLOCKS database utilizes the concept of blocks to identify a family of proteins, rather than relying on the individual sequences themselves (Henikoff and Henikoff, 1996). The idea of a block is derived from the more familiar notion of a motif, which usually refers to a conserved stretch of amino acids that confer a specific function or structure to a protein. When these individual motifs from proteins in the same family are aligned without introducing gaps, the result is a block, with the term block referring to the alignment, not the individual sequences themselves. Obviously, an individual protein can contain one or more blocks, corresponding to each of its fimctional or structural motifs. 

In the BLOCKS database (Henikoff et al., 1998), the motifs or blocks are created by automatically detecting the most highly conserved regions of each protein family. Initially three conserved amino acids are identified. The resulting blocks are then calibrated against SWISS-PROT to obtain a measure of the likelihood of a chance match. The database is accessible by keyword and sequence searches via the BLOCKS Web server at the Fred Hitchinson Cancer Research Center (http //www.blocks.fhcrc.org/). The Block includes the SWISS-PROT IDs of the constituent sequences, the start position of the fragment. 

BLOCKS Database of conserved regions in groups of proteins... 

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