INSECT (IN-silico SEarch for Co-occurring Transcription factors) is an easy-to-use and powerful web server for biologists analysing genomic sequence data for in silico cis-regulatory modules prediction and analysis.
PhylCRM is a new cis-regulatory module (CRM) prediction algorithm. PhylCRM combines data for individual motif occurances scored on an alignment using previously described MONKEY scoring sheme (Moses et al., Genome Biology 5, R98, 2004) into a single CRM prediction. PhylCRM can scan very long genomic sequences for candidate CRMs by quantifying both motif clustering and conservation across arbitrarily many genomes using an evolutionary model consistent with the phylogeny of the genomes.
MOPAT (Motif Pair Tree) identifies CRMs through the identification of motif modules, groups of motifs co-ccurring in multiple CRMs. It can identify orthologous CRMs without multiple alignments. It can also find CRMs given a large number of known motifs.
ModuleMaster is a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the program includes all necessary data and algorithms to perform every step to find CRMs.
bbq (Barbeques) is a command-line tool for discovering clusters of transcription factor binding sites that occur simultaneously in several genome sequences. Finding such clusters – which are sometimes also referred to as cis-regulatory modules – is done in a multiple-alignment-like fashion by solving a certain combinatorial and geometric optimization problem, the so-called best barbeque problem (explaining the name bbq). As opposed to classical, typically dynamic programming based, alignment procedures, the order of the binding sites’ occurences can be arbitrarily shuffled, so that bbq is the result of developing completely new algorithms.