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Bioinformatics Softwarez Tools

HOmo sapiens transcription factor COmprehensive MOdel COllection contains transcription factor (TF) binding models (motifs). The current release (v11) includes models for 680 human and 453 mouse TFs, new website, old website.

Transcription Factor Motif Location Toolbox is an interactive web application to scan DNA sequences for transcription factor binding sites (TFBS) with position weight matrices presented in HOCOMOCO model collection, see in action.

MAtrix CompaRisOn and PrEdicting Regulatory Functional Effect by Approximate P-value Estimation toolbox allows estimating motif P-values, comparing PWMs using natural Jaccard similarity measure and motif-based analysis of regulatory SNVs for mono- and dinucleotide PWMs, read more here and there.

ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. Now classic and dinucleotide versions come in a single updated package, read more.

Straightforward yet Powerful Rapid SuperAlphabet Representation Utilized for motif Search is as practical command-line ChIPMunk companion, read more.

EpiFactors is a database for epigenetic factors, corresponding genes and products,
read more.

GenometriCorr is an R package for spatial correlation of genome-wide interval datasets,
read more.