CoMoDis: composite motif discovery in mammalian genomes

CoMoDis: composite motif discovery in mammalian genomes

Specificity of mammalian gene regulatory regions is achieved to a large extent through the combinatorial binding of sets of transcription factors to distinct binding sites, discrete combinations of which are often referred to as regulatory modules. Identification and subsequent characterization of gene regulatory modules will be a key step in assembling transcriptional regulatory networks from ...

Motif Recognition in Genomes

A well known and mathematically well established approach to motif detection in DNA is that of Hidden Markov Models (HMM), where the model is trained using a set of training sequences. A major property of k-th order Markov models is their locality, i.e. the probability of a state depends only on the last k states. However, especially when 3-dimensional structure plays a role in the recognition ...

CMStalker: a combinatorial tool for composite motif discovery Supplementary materials

Mining Spatial Association Rules for Composite Motif Discovery

Motif discovery in biological sequences is an important field in bioinformatics. Most of the scientific research focuses on the de novo discovery of single motifs, but biological activities are typically co-regulated by several factors and this feature is properly reflected by higher order structures, called composite motifs, or cis-regulatory modules or simply modules. A module is a set of mot...

RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.

The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu ) offers specialized options for researchers dealing with plant transcriptional regulation. The website contains whole-sequenced genomes from species regularly updated from Ensembl Plants and other sources (currently 40), and supports an array of tasks frequently required for the analysis of regula...