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


BACKGROUND
http://blocks.fhcrc.org/
Henikoff
S
S
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. steveh@fhcrc.org
Henikoff
J G
JG
Pietrokovski
S
S
D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000235:genetics; D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D004265:DNA Helicases; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D016208:Databases, Factual; D006801:Humans; D008969:Molecular Sequence Data; D009687:Nuclear Proteins; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D017386:Sequence Homology, Amino Acid; D012984:Software; D012985:Software Design; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics
D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D011506:Proteins; C499336:SMARCA1 protein, human; C084011:SMARCA2 protein, human; D014157:Transcription Factors; D000251:Adenosine Triphosphatases; C084108:SMARCA4 protein, human; D004265:DNA Helicases