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Bioinformatics Advance Access originally published online on October 12, 2004
Bioinformatics 2005 21(6):811-816; doi:10.1093/bioinformatics/bti059
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

TRbase: a database relating tandem repeats to disease genes for the human genome

T. Boby , A.-M. Patch and S. J. Aves *

School of Biological and Chemical Sciences, Washington Singer Laboratories, University of Exeter Perry Road, Exeter EX4 4QG, UK

*To whom correspondence should be addressed.

Motivation: Tandem repeats are associated with disease genes, play an important role in evolution and are important in genomic organization and function. Although much research has been done on short perfect patterns of repeats, there has been less focus on imperfect repeats. Thus, there is an acute need for a tandem repeats database that provides reliable and up to date information on both perfect and imperfect tandem repeats in the human genome and relates these to disease genes.

Results: This paper presents a web-accessible relational tandem repeats database that relates tandem repeats to gene locations and disease genes of the human genome. In contrast to other available databases, this database identifies both perfect and imperfect repeats of 1–2000 bp unit lengths. The utility of this database has been illustrated by analysing these repeats for their distribution and frequencies across chromosomes and genomic locations and between protein-coding and non-coding regions. The applicability of this database to identify diseases associated with previously uncharacterized tandem repeats is demonstrated.

Availability: TRbase is available at http://trbase.ex.ac.uk/

Contact: S.J.Aves{at}exeter.ac.uk


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