Seminar, 01. April 2015, Ivo Grosse

01. April 2015, 14:15
Raum Louis Pasteur im HKI-Center for Systems Biology of Infection (Neubau A8_1_42)

Treasure hunt without treasure map – de-novo motif discovery in the jungle of DNA and RNA sequences

Prof. Dr. Ivo Grosse
(Institute of Computer Science at Martin Luther University Halle-Wittenberg and German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig)

De-novo motif discovery in DNA and RNA sequences has been a challenge since the early days of computational biology, and its importance has been increasing with the development of new experimental techniques and the ensuing flood of large-scale genomics and epigenomics data. One of the recurring questions debated controversially in wet labs and dry labs all over the world is to which extent intra-motif dependencies exist and to which extent they can improve de-novo motif discovery. Here, we address this question based on ENCODE ChIP-seq data, and we find that intra-motif dependencies exist in the majority of binding sites. Surprisingly, these intra-motif dependencies are not limited to first-order dependencies among directly adjacent nucleotides in many cases, and we find that higher-order dependencies up to order four can be utilised for an improved de-novo motif discovery.