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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), pp. 381-398.

Record type: Article

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.

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Published date: 2008

Identifiers

Local EPrints ID: 64707
URI: http://eprints.soton.ac.uk/id/eprint/64707
PURE UUID: 65ab0cb9-13ed-49ac-aad9-6273d6e2634e
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

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Date deposited: 09 Jan 2009
Last modified: 17 Jul 2017 14:12

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Contributors

Author: Nava E. Whiteford
Author: Niall J. Haslam
Author: Gerald Weber
Author: Adam Prügel-Bennett
Author: Cameron Neylon

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