Blocks Database  (http://blocks.fhcrc.org)

For Blocks+:	cd data-blplus/

For the Blocks database & associated files: cd data-blocks/

blocks.dat	Blocks Database
trees.dat	One phylogenetic tree in New Hampshire format for
		each group of proteins in the Blocks Database.
		Made by CLUSTALW from the block alignments.
cobbler.pros	One sequence from each group of proteins in the
		Blocks Database with embedded consensus residues
		selected from the block alignments.
maps.dat	Maps of blocks on the sequences for a group.
proweb.dat	Links from protein groups to curated documentation.
blinks.dat	Links from individual blocks to other protein family 
		collections based on comparing multiple alignments with LAMA.


For the Prints database in Blocks format: cd data-prints/

For the Pfam, Prodom & Domo groups included in Blocks+ with associated files:
	cd data-pfam/, data-prodom/, data-domo/

For the Blosum scoring matrices: cd blosum/

For the Protomat programs to make blocks: cd protomat/

For the UNIX version of BLIMPS to search the Blocks Database: cd blimps/


A partial list of citations for this work:

     For Protomat and the Blocks Database:
     Steven Henikoff & Jorja G. Henikoff, "Automated assembly of
     protein blocks for database searching", NAR 19:23 (1991),
     pp. 6565-6572.

     For position-based sequence weights used in Blocks:
     Steven Henikoff & Jorja G. Henikoff, "Position-based sequence
     weights", JMB 243 (1994), pp. 574-578..

     For Blosum scoring matrices:
     Steven Henikoff & Jorja G. Henikoff, "Amino acid             
     substitution matrices from protein blocks", PNAS 89          
     (1992), pp. 10915-10919.

     For COBBLER sequences derived from Blocks:
     Steven Henikoff & Jorja G. Henikoff, "Embedding strategies
     for effective use of information from multiple sequence
     alignments", Protein Science (1997), in press.

     For the Patmat/Blimps searching programs:
     James C. Wallace & Steven Henikoff, "PATMAT: a searching
     and extraction program for sequence, pattern and block
     queries and databases", CABIOS 8 (1992), pp. 249-254.

     For Prosite:
     Bairoch, A., "PROSITE: A dictionary of sites and patterns
     in proteins", NAR 20 (1992), pp. 2013-2018.

     For Motif:
     Hamilton O. Smith, Thomas M. Annau & Srinivasan
     Chandrasegaran, "Finding sequence motifs in groups of
     functionally related proteins", PNAS 87 (1990), pp. 826-830.

     For the Prints Database:
     Terri K. Attwood, et al, NAR 22(17) (1994), pp. 3590-3596.


If you have any questions, send electronic mail to 
     henikoff@blocks.fhcrc.org

--Jorja and Steve Henikoff