<p>Just a very quick question on promoter prediction software. Has anyone used any of the available tools and if so do you have any recommendations on a) the fastest b) the most accurate, and c) the best of both?</p>

<p>Here is a <a href='http://bip.weizmann.ac.il/toolbox/seq_analysis/promoters.html#searchtools'>list</a> of some I found! Are any of these scalable to whole-genome data? Are there any others not included here?</p>

<p>Of course if promoter prediction programs aren't the best way to retrieve these data (i.e. promoter sequences +/- first exon), then I'm open to suggestions :) I'm looking to do this for Hymenoptera (i.e. ant, bees, wasps).</p>

<p>Cheers,</p>

<p>Steve</p>

<p>You may also be interested in looking at some of the following from our labs Links page (<a href='http://facility.bioinformatics.ucr.edu/home/links'>http://facility.bioinformatics.ucr.edu/home/links</a>).</p>

<p>Software for Promoter Motif Discovery</p>

<ul>
<li><a href='http://rsat.ulb.ac.be/rsat'>Regulatory Sequence Analysis Tools (RSA)</a></li>
<li><a href='http://motifcut.stanford.edu/'>MotifCut (uses Maximum Density Subgraphs)</a></li>
<li><a href='http://www.cs.ucr.edu/%7Estelo/Verbumculus/'>Verbumculus</a></li>
<li><a href='http://bibiserv.techfak.uni-bielefeld.de/dialign/'>DiAlign (aligns sequences with local similarities)</a></li>
<li><a href='http://lagan.stanford.edu/'>LAGAN Alignment Toolkit Website</a></li>
<li><a href='http://abstract.cs.washington.edu/%7Eblanchem/FootPrinterWeb/FootPrinterInput.pl'>FootPrinter</a></li>
<li><a href='http://nemo.lbl.gov/rvista/rDetails.html'>rVista (human &amp; mouse)</a> (<strong>dead link</strong>)</li>
<li><a href='http://www.biobase.de/pages/who/biobase.html'>BioBase</a> (<strong>dead link</strong>)</li>
<li><a href='http://arep.med.harvard.edu/mrnadata/mrnasoft.html'>ScanACE AlignACE</a></li>
<li><a href='http://ural.wustl.edu/'>Consensus, ANN-Spec, Co-Bind, FoldAlign (Gary Stormo Lab)</a></li>
<li><a href='http://www.sdsc.edu/Research/biology/'>MEME META-MEME</a> (<strong>dead link</strong>)</li>
<li><a href='http://www-biology.ucsd.edu/labs/schroeder/'>MEME for Arabidopsis (Julian Schroeder Lab)</a> </li>
<li><a href='http://bayesweb.wadsworth.org/gibbs/gibbs.html'>The Gibbs Motif Sampler Homepage</a></li>
<li><a href='http://argon.cshl.org/ioschikz/gibbsDNA/mgibbsDNA-form.html'>Gibbs Motif Sampler, Coldspring Harbor</a></li>
<li><a href='http://www.esat.kuleuven.ac.be/%7Ethijs/Work/MotifSampler.html'>Motif Sampler</a></li>
<li><a href='http://genome-www4.stanford.edu/cgi-bin/ewing/oligoAnalysis.pl'>Stanford</a></li>
<li><a href='http://bioprospector.stanford.edu/'>BioProspector</a></li>
<li><a href='http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-geneid.html'>Collection at Genome Web</a> (<strong>dead link</strong>)</li>
<li><a href='http://rulai.cshl.edu/cgi-bin/regulatory/home.cgi?process=home'>Link Collection Page from CSL (Michael Zhang)</a></li>
</ul>

<p>Promoter Prediction</p>

<ul>
<li><a href='http://bimas.dcrt.nih.gov/molbio/signal/'>WWW Signal Scan</a> (<strong>dead link</strong>)</li>
<li><a href='http://www.fruitfly.org/seq_tools/promoter.html'>Neural Network Promoter Prediction</a></li>
<li><a href='http://zlab.bu.edu/%7Emfrith/nrra.html'>Nucleotide Regulatory Region Analysis</a></li>
<li><a href='http://sdmc.krdl.org.sg/promoter/Accuracy.html'>Accuracy</a> (<strong>dead link</strong>)</li>
<li><a href='http://zlab.bu.edu/%7Emfrith/cister.shtml'>Cister: Cis-element Cluster Finder</a></li>
<li><a href='http://argon.cshl.org/'>Human Promoter Prediction: Zhang Lab </a></li>
</ul>

<p>Promoter &amp; cis-Regulatory Element Databases</p>

<ul>
<li><a href='http://www.bioinformatics2.wsu.edu/cgi-bin/Athena/cgi/home.pl'>Athena</a></li>
<li><a href='http://www.epd.isb-sib.ch/'>Eukaryotic Promoter Database</a></li>
<li><a href='http://www.cbil.upenn.edu/tess/'>TESS : Transcription Element Search System</a></li>
<li><a href='http://zlab.bu.edu/%7Emfrith/HPD.html'>Human Promoter Database</a></li>
<li><a href='http://exon.cshl.org/cgi-bin/atprobe/atprobe.pl'>Arabidopsis thaliana Promoter Binding Element Database</a></li>
<li><a href='http://www.athamap.de/'>AthaMap (genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana)</a></li>
<li><a href='http://oberon.rug.ac.be:8080/PlantCARE/index.html'>PlantCare</a>  (<strong>dead link</strong>)</li>
<li><a href='http://www.dna.affrc.go.jp/htdocs/PLACE/'>PLACE</a></li>
<li><a href='http://arabidopsis.med.ohio-state.edu/AtcisDB/bindingSiteContent.jsp'>AGRIS (Arabidosis Gene Regulatory Information Server)</a></li>
<li><a href='http://www.gene-regulation.com/cgi-bin/pub/databases/transfac/search.cgi'>Transfac</a></li>
</ul>
