1 Applications Note cisExpress: Motif Detection in DNA Sequences

Motivation: One of the major challenges for contemporary bioinfor-matics is the analysis and accurate annotation of genomic datasets to enable extraction of useful information about the functional role of DNA sequences. This paper describes a novel genome-wide statis-tical 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 very large data sets 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 potentially applicable for use with a wide range of genomic databases for any species of interest. Availability: cisExpress is available at www.cisexpress.org Contact