Display Settings:

Format
Sort by

Send to:

Choose Destination

Results: 2

1.
Bioinformatics. 1999 Jun;15(6):471-9.

Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.

Author information

  • 1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. steveh@fhcrc.org

Abstract

MOTIVATION:

As databanks grow, sequence classification and prediction of function by searching protein family databases becomes increasingly valuable. The original Blocks Database, which contains ungapped multiple alignments for families documented in Prosite, can be searched to classify new sequences. However, Prosite is incomplete, and families from other databases are now available to expand coverage of the Blocks Database.

RESULTS:

To take advantage of protein family information present in several existing compilations, we have used five databases to construct Blocks+, a unified database that is built on the PROTOMAT/BLOSUM scoring model and that can be searched using a single algorithm for consistent sequence classification. The LAMA blocks-versus-blocks searching program identifies overlapping protein families, making possible a non-redundant hierarchical compilation. Blocks+ consists of all blocks derived from PROSITE, blocks from Prints not present in PROSITE, blocks from Pfam-A not present in PROSITE or Prints, and so on for ProDom and Domo, for a total of 1995 protein families represented by 8909 blocks, doubling the coverage of the original Blocks Database. A challenge for any procedure aimed at non-redundancy is to retain related but distinct families while discarding those that are duplicates. We illustrate how using multiple compilations can minimize this potential problem by examining the SNF2 family of ATPases, which is detectably similar to distinct families of helicases and ATPases.

AVAILABILITY:

http://blocks.fhcrc.org/

PMID:
10383472
[PubMed - indexed for MEDLINE]
Free full text
Icon for HighWire
2.
Nucleic Acids Res. 2000 Jan 1;28(1):228-30.

Increased coverage of protein families with the blocks database servers.

Author information

  • 1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.

Abstract

The Blocks Database WWW (http://blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PROSITE and PRINTS. Other new features include improved Block Searcher statistics, searching with NCBI's IMPALA program and 3D display of blocks on PDB structures.

PMID:
10592233
[PubMed - indexed for MEDLINE]
PMCID:
PMC102407
Free PMC Article
Icon for HighWire Icon for PubMed Central

Supplemental Content

Write to the Help Desk