Bioinformatics Links Directory : Gene Regulation

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

WordSpy - (Found July 2, 2008 )

WordSpy allows the user to search for over-represented words in a set of sequences and to search for discriminative words using negative sequence data. WordSpy employs this functionality as a means to search for transcription factor binding motifs.
http://cic.cs.wustl.edu/wordspy/

ZiFiT - (Found July 2, 2008 )

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences; free registration is required.
http://bindr.gdcb.iastate.edu/ZiFiT/

T-Reg Comparator - (Found July 2, 2008 )

T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).
http://treg.molgen.mpg.de/

SynoR - (Found July 2, 2008 )

SynoR searches vertebrate genomes for synonymous regulatory elements.
http://synor.dcode.org/

RNAhybrid - (Found July 2, 2008 )

RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.
http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

RSAT - (Found July 2, 2008 )

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities.
http://rsat.ccb.sickkids.ca/

rVISTA - (Found July 2, 2008 )

Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.
http://rvista.dcode.org/

SCOPE - (Found July 2, 2008 )

SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences.
http://genie.dartmouth.edu/scope/

SITECON - (Found July 2, 2008 )

Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.
http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/

SiteSeer - (Found July 2, 2008 )

SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.
http://rocky.bms.umist.ac.uk/SiteSeer/