Extract Promoter Sequences
5UTR	http://www.google.com/search?hl=en&q=set+default+file+view+in+windows+XP
bdgp Neural Network Promoter Prediction	http://www.fruitfly.org/seq_tools/promoter.html
biobase	http://www.gene-regulation.com/pub/programs.html
BioinformaticsOnline.org	http://www.bioinformaticsonline.org/links/ch_09_t_6.html
BioProspector	http://robotics.stanford.edu/~xsliu/BioProspector/
cisred TF motifs	http://www.cisred.org/
cread Comprehensive Regulatory Element Analysis and Discovery	http://rulai.cshl.edu/cread/index.shtml
DBTSS HOME	http://dbtss.hgc.jp/index.html
DNA to protein translation	http://insilico.ehu.es/translate/
EBI Tools Transeq	http://www.ebi.ac.uk/emboss/transeq/
EBI Tools Transeq (Imported)	http://www.ebi.ac.uk/Tools/emboss/transeq/index.html
EXALIN — mRNA to genomic alignment	http://blast.wustl.edu/exalin/
ExPASy - Translate tool	http://ca.expasy.org/tools/dna.html
Gene Regulation	http://www.gene-regulation.com/pub/databases.html
Genomatix Promoter Database	http://www.genomatix.de/online_help/help_gpd/gpd_help.html
genomatrix	http://www.genomatix.de/online_help/help_matinspector/matinspector_help.html
great Genomic Regions Enrichment of Annotations Tool, Bejerano Lab, Stanford University	http://great.stanford.edu/
Harvard map translate	http://pga.mgh.harvard.edu/web_apps/web_map/start
http--www.gene-regulation.com-pub-programs-cma-CMA.html	http://www.gene-regulation.com/pub/programs/cma/CMA.html
inclusive bioi	http://homes.esat.kuleuven.be/~dna/BioI/Software.html
Index of -goldenPath-hg19-bigZips	http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
Index of -goldenPath-mm9-bigZips	http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/
JustBio Home Page	http://www.justbio.com/index.php
JustBio Translator	http://www.justbio.com/translator/index.php
matbase Introduction	http://www.genomatix.de/online_help/help_matbase/matbase_help.html
meta WEB server	http://genome.imim.es/software/meta/meta.html
mmeta WEB server	http://genome.imim.es/software/mmeta/mmeta.html
moduleminer	http://www.kuleuven.be/bioinformatics/
neibank Informatics Resources Available to NEI Researchers	http://neibank.nei.nih.gov/resources/resources.shtml
Online Analysis Tools - Translation	http://molbiol-tools.ca/Translation.htm
opossum Human SSA - Default Mode	http://www.cisreg.ca/cgi-bin/oPOSSUM/opossum
ORF Finder	http://www.ncbi.nlm.nih.gov/gorf/gorf.html
P-Match	http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi
rVista 2.0 Identification of Evolutionary Conserved Transcription Factor Binding Sites	http://rvista.dcode.org/
Smart BLAST	http://blast.ncbi.nlm.nih.gov/smartblast/smartBlast.cgi
stamp A tool-kit for DNA motif comparison	http://www.benoslab.pitt.edu/stamp/
targeted genes	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm
tfacts	http://www.tfacts.org/
TFM suite	http://bioinfo.lifl.fr/TFM/
tfsearch Searching Transcription Factor Binding Sites	http://www.cbrc.jp/research/db/TFSEARCH.html
toucan 2	http://homes.esat.kuleuven.be/~saerts/software/toucan.php
TRANSFACdatabase 7.0 - public	http://www.gene-regulation.com/cgi-bin/pub/databases/transfac/search.cgi
TransFind	http://transfind.sys-bio.net/
Translate Nucleic Acid Sequence Tool	http://biotools.umassmed.edu/cgi-bin/biobin/transeq
Translation lundberg	http://bio.lundberg.gu.se/edu/translat.html
TRED	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home
TRED Promoter Database	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchPromForm
Upstream sequences for human and mouse genes	http://arep.med.harvard.edu/labgc/adnan/hsmmupstream/
UTR scan	http://itbtools.ba.itb.cnr.it/utrscan
WIBR UTR extractor	http://jura.wi.mit.edu/bioc/tools/utrs/