Bioinformatics, Vol 14, 144-150, Copyright © 1998 by Oxford University Press
J Park and SA Teichmann
MOTIVATION: Large-scale determination of relationships between the proteins
produced by genome sequences is now common. All protein sequences are
matched and those that have high match scores are clustered into families.
In cases where the proteins are built of several domains or duplication
modules, this can lead to misleading results. Consider the very simple
example of three proteins: 1, formed by duplication modules A and B; 2,
formed by duplication modules B' and C; and 3, formed by duplication
modules C' and D. Duplication modules B and B' are homologous, as are C and
C'. Matching the sequences of 1, 2 and 3 followed by simple single-linkage
clustering would put all three in the same family, even though proteins 1
and 3 are not related. This is because the different parts of 2 match 1 and
3. This paper describes a procedure, DIVCLUS, that divides such complex
clusters of partially related sequences into simple clusters that contain
only related duplication modules. In the example just given, it would
produce two groups of sequences: the first with domains B of sequence 1 and
B of sequence 2, and the second with domain C of sequence 2 and C of
sequence 3. DIVCLUS is part of a package called GEANFAMMER, for GEnome
ANalysis and protein FAMily MakER. The package automates the detection of
families of duplication modules from a protein sequence database. RESULTS:
DIVCLUS has been applied to the division of single-linkage clusters
generated from the protein sequences of six completely sequenced bacterial
genomes. Out of 12 013 genes in these six genomes, 4563 single- and
multi-domain sequences formed 1071 complex clusters. Application of the
DIVCLUS program resolved these clusters into 2113 clusters corresponding to
single duplication modules. AVAILABILITY: The perl5 program and its
documentation are available at the following address:
http://www.mrc-lmb.cam.ac.uk/genomes/ and by anonymous ftp at
ftp.mrc-lmb.cam.ac.uk in the directory /pub/genomes/Software/. CONTACT:
sat@mrc-lmb.cam.ac.uk; jong@mrc-lmb. cam.ac.uk
ARTICLES
DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins
MRC Laboratory of Molecular Biology, Cambridge, UK.
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