BROWSE

Related Researcher

Author's Photo

Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

ITEM VIEW & DOWNLOAD

DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins

Cited 44 times inthomson ciCited 44 times inthomson ci
Title
DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins
Other Titles
DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins
Author
Bhak, Jong HwaTeichmann, SA
Keywords
SEQUENCE; GENOME
Issue Date
1998
Publisher
OXFORD UNIV PRESS
Citation
BIOINFORMATICS, v.14, no.2, pp.144 - 150
Abstract
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 al-e built of several domains or duplication modules, this can lead to misleading results. Consider the very simple example of three proteins: I, 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 pal fs 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 I 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 fi-om a protein sequence database. Results: DIVCLUS has been applied to the division of single-linkage clusters generated from the protein sequences of sh completely sequenced bacterial genomes. Our 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
URI
Go to Link
DOI
10.1093/bioinformatics/14.2.144
ISSN
1367-4803
Appears in Collections:
BME_Journal Papers
Files in This Item:
Bioinformatics-1998-Park-144-50.pdf Download

find_unist can give you direct access to the published full text of this article. (UNISTARs only)

Show full item record

qrcode

  • mendeley

    citeulike

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

MENU