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Search with a protein sequence against BLOCKS library
BLOCKS [1, 2] are multiply aligned ungapped segments
corresponding to the most highly conserved regions of proteins.
This server uses the BLIMPS  program to search a protein
sequence against the BLOCKS database. BLIMPS (BLocks IMProved Searcher) is a searching tool that
scores asequence against blocks or a block against sequences. BLIMPS augments
the block functions of PATMAT  for UNIX, which is no longer supported
The blocks for the BLOCKS Database are made automatically by looking for the most highly
conserved regions in groups of proteins documented in the Prosite Database. The Prosite pattern
for a protein group is not used in any way to make the BLOCKS Database and the pattern may or
may not be contained in one of the blocks representing a group. These blocks are then calibrated
against the SWISS-PROT database to obtain a measure of the chance distribution of matches. It
is these calibrated blocks that make up the BLOCKS Database.
(From the description of http://blocks.fhcrc.org
During the search each entry in BLOCKS database, a set of blocks is converted to
a position-specific score matrix (profile). This matrix is used to score the motif found in the query sequence. The entry in the BLOCKS database has a value representing 99.5 % of the score
of true negative sequence placed on BL line.  Each raw score
is divided by this 99.5 % score and multiplied by 1000. Thus, a derived score of 1000 means that
match would be at the 99.5 % false matches which means scores less than around 1000 are
therefore probably not important.
The found motifs are listed in a table. From the AC numbers of BLOCKS you can jump into DBGET to look at the hits as well as related informations precisely. Under Position (Score) column of the table the position (start and end sequence numbers) and
the scores of found motifs are listed. Click Detail bottun to see actual positions of the blocks motif along the query sequence . (shown
Below a sample output table of the search is shown. Click the images to get detailed results discribed above.
J.G. Henikoff, E.A. Greene, S. Pietrokovski and S. Henikoff
"Increased coverage of protein families with the blocks database servers"
Nucl. Acids Res. 28(1):228-230, 2000.
2. Henikoff S., Henikoff J.G. Pietrokovski S.
Blocks+: A non-redundant database of protein alignment blocks dervied from multiple compilations
Bioinformatics 15:471-479 (1999)
- 3. Wallace J.C., Henikoff S.
PATMAT: A searching and extraction program for sequence, pattern, and block queries and databases.
CABIOS , 8:249-254 (1992)
4. Henikoff S., Henikoff J.G.
Automated assembly of protein blocks for database searching
Nucleic Acid Res., 19:6565-6572 (1991)