Blocks Database Version 11.0, July 1998
Copyright 1998 by Fred Hutchinson Cancer Research Center
1100 Fairview AV N, A1-162, Seattle, WA 98109
Version 11.0 of the Blocks Database consists of 4034 blocks representing 994 groups documented in PROSITE 15 keyed to SWISS-PROT 36 obtained from the ExPASy server . When appropriate, Version 11.0 combines sequences from different prosite.dat entries when they have the same prosite.doc entry; e.g. PS00094 and PS00095 are both documented by PDOC0089 so sequences from both entries were used to make the blocks for BL00094.
The Blocks Database was constructed by the PROTOMAT system (S Henikoff & JG Henikoff, "Automated assembly of protein blocks for database searching", NAR (1991) 19:6565-6572) using the MOTIF algorithm (HO Smith, et al, "Finding sequence motifs in groups of functionally related proteins", PNAS (1990) 87:826-830) as implemented in Block Maker.
Although the PROSITE pattern is not used in any way to make the Blocks Database, major releases of the Blocks Database are based on major releases of PROSITE to take of advantage of the protein groups documented there: Blocks representing a PROSITE group may or may not contain the pattern. Check SWISS-FLASH for news about PROSITE and SWISS-PROT.
(Manuscript in PDF format)
For searching, the protein groups in the Blocks Database are supplemented with groups from other collections for a total of 10,532 blocks from 2334 groups:
2868 blocks made by Terri Attwood from 448 groups documented in PRINTS 25.0 but not represented in the Blocks Database are included in searches.
2258 blocks made by PROTOMAT from 536 groups documented in PFAM 4.4 but not represented in the Blocks or PRINTS Databases are included in searches.
1066 blocks made by PROTOMAT from 273 groups documented in PRODOM 99.1 entries 1-4999 but not represented in the Blocks, PRINTS or PFAM Databases are included in searches.
306 blocks made by PROTOMAT from 83 groups documented in DOMO 2.0 entries 1-1999 but not represented in the Blocks, PRINTS, PFAM or PRODOM Databases are included in searches.
To avoid the over-representation of compositionally biased blocks in search results, this subset of the Blocks+ database excludes several biased blocks. It may give better results, especially with DNA queries.
Page last modified