Visualising the repeat structure of genomic sequences


Whiteford, Nava E., Haslam, Niall J., Weber, Gerald, Prügel-Bennett, Adam, Essex, Jonathan W. and Neylon, Cameron (2008) Visualising the repeat structure of genomic sequences. Complex Systems, 17, (4), 381-398.

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Description/Abstract

Repeats are a common feature of genomic sequences and much remains
to be understood of their origin and structure. The identification of repeated strings in genomic sequences is therefore of importance for a variety of applications in biology.
In this paper a new method for finding all repeats and visualising them in a two dimensional plot is presented. The method is first applied to a set of constructed sequences in order to develop a comparative
framework. Several complete genomes are then analysed, including the whole human genome.
The technique reveals the complex repeat structure of genomic sequences.
In particular, interesting differences in the repeat character of the coding and non-coding regions of bacterial genomes are noted. The method allows fast identification of all repeats and easy intergenome comparison. In doing this the plot effectively creates a signature of a sequence which allows some classes of repeat present in a sequence to be identified by simple visual inspection.
To our knowledge this is the first time all exact repeats have been visualised in a single plot that highlights the degree to which repeats occur within a genomic sequence, giving an indication of the important role repeats play. From this it is clear that large scale repeat analysis remains an important and unsolved problem in Bioinformatics.

Item Type: Article
ISSNs: 0891-2513 (print)
Related URLs:
Subjects: Q Science > Q Science (General)
Q Science > QR Microbiology > QR355 Virology
Divisions: University Structure - Pre August 2011 > School of Chemistry
University Structure - Pre August 2011 > School of Electronics and Computer Science > Intelligence, Agents, Multimedia
ePrint ID: 64707
Date Deposited: 09 Jan 2009
Last Modified: 27 Mar 2014 18:46
URI: http://eprints.soton.ac.uk/id/eprint/64707

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