Dataset Information

CisExpress: motif detection in DNA sequences.

ABSTRACT:

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 www.cisexpress.org.

SUBMITTER: Triska M

PROVIDER: S-EPMC3740630 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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Publications

cisExpress: motif detection in DNA sequences.

Triska Martin M Grocutt David D Southern James J Murphy Denis J DJ Tatarinova Tatiana T

Bioinformatics (Oxford, England) 20130621 17

<h4>Motivation</h4>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 ...[more]

PMID: 23793750

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