Bioinformatics Links Directory : Gene RegulationThis section contains links to tools and resources for predicting gene regulation, such as promoter analysis.NXSensor- (Found July 2, 2008 ) Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.http://www.sfu.ca/~ibajic/NXSensor/ PromoterPlot- (Found July 2, 2008 ) PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTAAffymetrix IDs can also be used as input for a local installation of the tool.http://promoterplot.fmi.ch/ PromoterWise- (Found July 2, 2008 ) Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.http://www.ebi.ac.uk/Wise2/promoterwise.html PROSITE- (Found July 2, 2008 ) Database of protein families and domains defined from SwissProt database; consider also checking specific motif databases such as PhosphoBase.http://us.expasy.org/prosite/ PubGene- (Found July 2, 2008 ) Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package.http://www.pubgene.com/public.htm Readout- (Found July 2, 2008 ) Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.http://gibk26.bse.kyutech.ac.jp/jouhou/readout/ REDfly- (Found July 2, 2008 ) Regulatory Element Database for Drosophila (REDfly) is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). REDfly seeks to include all experimentally verified fly CRMs along with their DNA sequence, their associated genes, and the expression patterns they direct.http://redfly.ccr.buffalo.edu/?content=/search.php REDUCE- (Found July 2, 2008 ) REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.http://bussemaker.bio.columbia.edu/reduce/ RegRNA- (Found July 2, 2008 ) Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5'-UTR and 3'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donoracceptor sites; RNA structural features; and miRNA target sites.http://regrna.mbc.nctu.edu.tw/ RibEx- (Found July 2, 2008 ) Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conservedhttp://www.ibt.unam.mx/biocomputo/RibEx.html |