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Search with a protein sequence against BLOCKS library

OVERVIEW

BLOCKS [1, 2] are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
" 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)
This server uses the BLIMPS [3] 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 [3] for UNIX, which is no longer supported by FHCRC.

SCORE

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. [4] 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.

RESULTS

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 in red)

OUTPUT

Below a sample output table of the search is shown. Click the images to get detailed results discribed above.

blocks-res1
res2 res3

References

1. 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.
PubMed: 10592233

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)
PubMed: 10383472

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)
PubMed: 1633566

4. Henikoff S., Henikoff J.G.
Automated assembly of protein blocks for database searching
Nucleic Acid Res., 19:6565-6572 (1991)
PubMed: 1754394