The Genomics of Transcriptional Regulation
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[
Alignment Tools || Motif Finding || Comparative Genomics || Transcription Factor Analysis || General Software ]

Multiple Sequence Alignment Tools

ClustalW -- ClustalW server at EBI.
T-Coffee -- Method for multiple sequence alignments.
MAFFT -- Method for sequence alignment based on fast Fourier transform.
POA -- Partial Order Alignment algorithm.
Dialign -- Segment-to-segment alignment method.
MAVID -- Multiple alignment server.

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Motif Finding Algorithms

DME -- Discriminating Matrix Enumerator.
DWE -- Discriminating Word Enumerator.
Consensus -- Determines consensus patterns in unaligned sequences - uses matrix representation of consensus patterns.
MEME -- Discovers motifs in related sequences.
Gibbs Sampler -- A Gibbs Sampler algorithm for finding motifs.
Co-Bind (and others) -- Searches for TF binding sites for cooperatively binding TFs.
REDUCE -- Regulatory Element Detection Using Correlation with Expression -- Motif finding algorithm that relates motif information to microarray data.
MDScan -- Motif finding algorithm developed to aid in Chromatin Immunoprecipitation experiments.
BioProspector -- Algorithm to find motifs in co-expressed genes.
Motif Regressor -- Program for finding DNA sequence motifs.
BMC -- Bayesian motif clustering algorithm.
FastM at Genomatix -- Generate models for regulatory sequences utlizing TRANSFAC matrices.
MatInspector at Genomatix -- Search for new TF binding sites using TRANSFAC matrices.
Signal Scan -- Find and list homologies of published signal sequences with input DNA sequence.
YMF and FindExplanators -- Motif discovery programs.
AlignACE -- Motif finding algorithm.
Ann-spec 1.0 -- Motif search program for yeast and human sequences.
GLAM -- Gapless Local Alignment of Multiple Sequences
Improbizer -- Program to search for motifs in DNA and RNA using a variation of the EM algorithm
MotifSampler -- Motif finding algorithm using Gibbs sampling.
SeSiMCMC Sequence Similarities by Markov Chain Monte-Carlo -- A Gibbs sampling algorithm that considers the possibility of site absences.
Motif Analysis Workbench -- Collection of tools for motif analysis in S. cerevisiae.
ConSite -- Tool for finding transcription factor binding sites shared by two sequences
MScan -- Algorithm for detecting regulatory modules.
Cluster-Buster -- Find clusters of pre-specified motifs in sequences.
Creme - Web-server for indentifying cis-regulatory modules.

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Comparative Genomics Tools

PatternHunter -- Homology search algorithm.
VISTA -- Set of tools for comparative genomics.
Footprinter -- Phylogenetic footprinting software.
Bayesian Phylogenetic Footprint -- The Bayes aligner.
PIPMaker -- Software for local sequence alignment and percentage identity plots.
LAGAN Toolkit -- Set of alignment programs for comparative genomics.
PhyloCon -- Phylogentic motif discovery software.

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Transcription Factor Analysis

TFBind -- Software for searching for transcription factor binding sites.
TESS -- Transcription Element Search System -- Web based software for predicting transcription factor binding sites.
TFSearch -- Software for finding transcription factor binding sites.

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General Regulatory Network Tools

Toucan -- Provides tools for analysis of regulatory elements in metazoan genomes.
RSAT -- Regulatory Sequence Analysis Tools -- Set of tools for analysis of regulatory elements, specifically designed for intergenic sequences.
Match, etc. -- TRANSFAC software using various methods to search for TFBS.
TRANSFAC 6.0 - Public Public version of Transfac
ZLAB -- Dr. Zhiping Weng's site at Boston University - a variety of gene regulation tools. Plus, many links to other sites.
Fun Site -- Tools for the analysis of regulatory sequence in eukaryotes.
rVista -- Regulatory element search algorithm that combines database searches with comparative sequence analysis.

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Michael Zhang Lab , Cold Spring Harbor Laboratory, all rights reserved
Questions/suggestions email: dschones@cshl.edu