Skip Navigation



Bioinformatics Advance Access published online on October 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti059
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/6/811    most recent
bti059v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Boby, T.
Right arrow Articles by Aves, S. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Boby, T.
Right arrow Articles by Aves, S. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received April 1, 2004
Revised August 21, 2004
Accepted September 20, 2004

Article

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

T. Boby 1, A.-M. Patch 1, and S. J. Aves 1*

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

* To whom correspondence should be addressed. E-mail: S.J.Aves{at}exeter.ac.uk.


  Abstract

Motivation: Tandem repeats are associated with disease genes, play an important role in evolution and are important in genomic organisation 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 repeat 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 to 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 uncharacterised tandem repeats is demonstrated.

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
A. Merkel and N. Gemmell
Detecting short tandem repeats from genome data: opening the software black box
Brief Bioinform, September 1, 2008; 9(5): 355 - 366.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
D. Ames, N. Murphy, T. Helentjaris, N. Sun, and V. Chandler
Comparative Analyses of Human Single- and Multilocus Tandem Repeats
Genetics, July 1, 2008; 179(3): 1693 - 1704.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. B. Mudunuri and H. A. Nagarajaram
IMEx: Imperfect Microsatellite Extractor
Bioinformatics, May 15, 2007; 23(10): 1181 - 1187.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
A.-M. Patch and S. J. Aves
Fingerprinting fission yeast: polymorphic markers for molecular genetic analysis of Schizosaccharomyces pombe strains
Microbiology, March 1, 2007; 153(3): 887 - 897.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
A. Shelenkov, K. Skryabin, and E. Korotkov
Search and Classification of Potential Minisatellite Sequences from Bacterial Genomes
DNA Res, January 1, 2006; 13(3): 89 - 102.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.