DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

• DOI: 10.1186/s12859-018-2215-1
• Publication Date: 2018-06-11T09:19:55Z
• Authors: Chadi Saad; Laurent Noé; Hugues Richard; Julie Leclerc; Marie-Pierre Buisine; Hélène Touzet; Martin Figeac
• Keywords: Motif (music)

Discovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because the increasing number potential applications. However, it remains a difficult challenge, especially with huge quantity data generated by high throughput sequencing technologies. To overcome this problem, existing tools use greedy algorithms and probabilistic approaches to find reasonable time. Nevertheless these lack sensitivity have difficulties coping rare subtle motifs. We developed DiNAMO (for MOtif), new software based on exhaustive efficient algorithm for IUPAC motif discovery. evaluated synthetic real datasets two different applications, namely ChIP-seq peaks Systematic Sequencing Error analysis. proves compare favorably other methods robust noise. shown that can serve as tool search degenerate exact manner using models. be used scanning mode sliding windows or fixed position mode, which makes suitable numerous https://github.com/bonsai-team/DiNAMO .