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Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

Memon, FN and Owen, AM and Sanchez-Graillet, O and Upton, GJG and Harrison, AP (2010) 'Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.' Journal of integrative bioinformatics, 7 (2). 111 - ?. ISSN 1613-4516

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Abstract

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays.

Item Type: Article
Subjects: Q Science > QA Mathematics
Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health > Mathematical Sciences, Department of
Depositing User: Jim Jamieson
Date Deposited: 09 Dec 2011 15:31
Last Modified: 06 Feb 2019 00:15
URI: http://repository.essex.ac.uk/id/eprint/1748

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