The University of Southampton
University of Southampton Institutional Repository

A fast algorithm for the construction of universal footprinting templates in DNA

Record type: Article

We introduce and give a complete description of a new graph to be used for DNA sequencing questions. This graph has the advantage over the classical de Bruijn graph that it fully accounts for the double stranded nature of DNA, rather than dealing with single strands. Technically, our graph may be thought of as the quotient of the de Bruijn graph under the natural involution of sending a DNA strand to its complementary strand. However, this involution has fixed points, and this complicates the structure of the quotient graph which we have therefore modified herein. As an application and motivating example, we give an efficient algorithm for constructing universal footprinting templates for n-mers. This problem may be formulated as the task of finding a shortest possible segment of DNA which contains every possible sequence of base pairs of some fixed length n. Previous work by Kwan et al has attacked this problem from a numerical point of view and generated minimal length universal footprinting templates for n=2, 3, 5, 7, together with unsubstantiated candidates for the case n=4. We show that their candidates for n=4 are indeed minimal length universal footprinting templates.

PDF dna_final.pdf - Author's Original
Download (382kB)

Citation

Anderson, James W., Fox, Keith R. and Niblo, Graham A. (2006) A fast algorithm for the construction of universal footprinting templates in DNA Journal of Mathematical Biology, 52, (3), pp. 307-342. (doi:10.1007/s00285-005-0357-z).

More information

Published date: 1 March 2006
Keywords: DNA sequencing, universal footprinting template, de bruijn graph, eulerian graphs

Identifiers

Local EPrints ID: 29879
URI: http://eprints.soton.ac.uk/id/eprint/29879
ISSN: 0303-6812
PURE UUID: 0bf102e4-2b32-49a3-b296-5d093af0caaa
ORCID for James W. Anderson: ORCID iD orcid.org/0000-0002-7849-144X
ORCID for Keith R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 11 May 2006
Last modified: 17 Jul 2017 15:56

Export record

Altmetrics


Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×