CisExpress: Motif detection in DNA sequences

Martin Triska, David Grocutt, James Southern, Denis J. Murphy, Tatiana Tatarinova

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid


MOTIVATION: One of the major challenges for contemporary bioinformatics is the analysis and accurate annotation of genomic datasets to enable extraction of useful information about the functional role of DNA sequences. This article describes a novel genome-wide statistical approach to the detection of specific DNA sequence motifs based on similarities between the promoters of similarly expressed genes. This new tool, cisExpress, is especially designed for use with large datasets, such as those generated by publicly accessible whole genome and transcriptome projects. cisExpress uses a task farming algorithm to exploit all available computational cores within a shared memory node. We demonstrate the robust nature and validity of the proposed method. It is applicable for use with a wide range of genomic databases for any species of interest.

AVAILABILITY: cisExpress is available at
Iaith wreiddiolSaesneg
Tudalennau (o-i)2203-2205
Nifer y tudalennau3
Rhif cyhoeddi17
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 1 Medi 2013

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