Description:
<jats:title>Abstract</jats:title>
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<jats:title>Motivation</jats:title>
<jats:p>The discovery of sequence motifs mediating DNA-protein binding usually implies the determination of binding sites using high-throughput sequencing and peak calling. The determination of peaks, however, depends strongly on data quality and is susceptible to noise.</jats:p>
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<jats:title>Results</jats:title>
<jats:p>Here, we present a novel approach to reliably identify transcription factor-binding motifs from ChIP-Seq data without peak detection. By evaluating the distributions of sequencing reads around the different k-mers in the genome, we are able to identify binding motifs in ChIP-Seq data that yield no results in traditional pipelines.</jats:p>
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<jats:title>Availability and implementation</jats:title>
<jats:p>NoPeak is published under the GNU General Public License and available as a standalone console-based Java application at https://github.com/menzel/nopeak.</jats:p>
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<jats:title>Supplementary information</jats:title>
<jats:p>Supplementary data are available at Bioinformatics online.</jats:p>
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