Bioinformatics, Vol 15, 471-479, Copyright © 1999 by Oxford University Press
S Henikoff, JG Henikoff and S Pietrokovski
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/
ARTICLES
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. steveh@fhcrc.org
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