Bioinformatics Links Directory : Gene Regulation

This section contains links to tools and resources for predicting gene regulation, such as promoter analysis.

CisMols - (Found July 2, 2008 )

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.
http://cismols.cchmc.org/

cisRED - (Found July 2, 2008 )

cisRED is a database system for genome-scale computational discovery of regulatory elements.
http://www.cisred.org/

Cluster Buster - (Found July 2, 2008 )

Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.
http://zlab.bu.edu/cluster-buster/

CMA - (Found July 2, 2008 )

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.
http://www.gene-regulation.com/pub/programs/cma/CMA.html

FirstEF - (Found July 2, 2008 )

First Exon Finder (FirstEF) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.
http://rulai.cshl.org/tools/FirstEF/

MYBS - (Found July 2, 2008 )

MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.
http://cg1.iis.sinica.edu.tw/~mybs/index.php

MatInspector - (Found July 2, 2008 )

Search for potential transcription factor binding sites in your own sequences using TRANSFAC matrices; free for non-commercial use.
http://www.gene-regulation.com/pub/programs.html#matinspector

MDscan - (Found July 2, 2008 )

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.
http://robotics.stanford.edu/~xsliu/MDscan/

MelinaII - (Found July 2, 2008 )

MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.
http://melina2.hgc.jp/public/index.html

MEME - (Found July 2, 2008 )

MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.
http://meme.nbcr.net/meme/intro.html