CMStalker: A Combinatorial Tool for Composite Motif Discovery

CMStalker: a combinatorial tool for composite motif discovery Supplementary materials

Motif Tool Manager: a web-based framework for motif discovery

MOTIVATION Motif Tool Manager is a web-based framework for comparing and combining different approaches to discover novel DNA motifs. It comes with a set of five well-known approaches to motif discovery. It provides an easy mechanism for adding new motif finding tools to the framework through a web-interface and a minimal setup of the tools on the server. Users can execute the tools through the...

A Combinatorial Approach for Motif Discovery in Unaligned DNA Sequences

Motif (conserved pattern) modelling and finding in unaligned DNA sequences is a fundamental problem in computational biology with important applications in understanding gene regulation. Biological approaches for this problem are tedious and time-consuming. Large amounts of genome sequence data and gene expression micro-array data let us solve this problem computationally. Most computer science...

The SiteSeeker Motif Discovery Tool

In this paper we describe some utilizing conditions of a recently published tool that offers two basic functions for the classical problem of discovering motifs in a set of promoter sequences. For the first it is assumed that not necessarily all of the sequences possess a common motif of given length l. In this case, CHECKPROMOTER allows an exact identification of maximal subsets of related pro...

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 ...