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TFBSs resources
 
 
Created on: 04-Jan-2011   Last updated on: 10-Jul-2011 |  How to cite this?
Total resources - 105
A compilation of promoter prediction resources
Dilna J.P and Tinsu Mathew (Correspondence Acharya KK: kshitish@ibab.ac.in)
 Click here for additional comparative study/note

S.NoResources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
1 GENSCAN
http://genes.mit.edu/GENSCAN.html		 Mainly a gene-structure identification tool.
Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997 Apr 25;268(1):78-94. PubMed PMID: 9149143.
1997
30
 Creators of the tool clearly state that promoter prediction by it is NOT reliable.
2 MEME - Multiple Em for Motif Elicitation
http://meme.sdsc.edu/meme/intro.html		 Identifies repeated, ungapped sequence pattern in the gene. Also, finds motifs and compare with the databases of known motifs to find matches.
Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73. PubMed PMID: 16845028; PubMed Central PMCID: PMC1538909.
2006
41
 Not an exclusive tool for promoter prediction, designed for short pattern recognition in general by statistical measures. Hence, it can be useful in identifying novel TFBSs, if any. Caution: results may go to the spam folder!
3 MatInspector
http://www.genomatix.de/solutions/genomatix-software-suite.html		 Involves TFBS prediction, which can be used as a prerequisite for promoter detection. Claims to avoid false-positive and redundant matches. Identifies TFBSs and promoters.
Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics. 2005 Jul 1;21(13):2933-42. Epub 2005 Apr 28. PubMed PMID: 15860560.
2005
52
 Currently a module within the Genomatix Software Suite. The website in the 2005 abstract actually links to help-pages. Free for academics. MatInspector latest release: 8.0.5: September 2011
4 TESS - Transcription Element Search System
http://www.cbil.upenn.edu/cgi-bin/tess/tess		 Identifies TFBSs using consensus strings and PWMs from TRANSFAC, JASPAR, etc. User-input sequences are also accepted.
Schug J. Using TESS to predict transcription factor binding sites in DNA sequence. Curr Protoc Bioinformatics. 2008 Mar;Chapter 2:Unit 2.6. PubMed PMID: 18428685.
2008
62
 Not available at the website but source code is available at: http://www.cbil.upenn.edu/downloads/
5 NNPP - Neural Network Promoter Prediction
http://www.fruitfly.org/seq_tools/promoter.htm		 Finds transcription promoters.
Reese MG. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem. 2001 Dec;26(1):51-6. PubMed PMID: 11765852.
2001
67
 Thhe current URL shows error and redirects to another page, BDGP site. Online/ downloadable.
6 TRANSCompel
http://www.gene-regulation.com/pub/databases.html#transcompel		 Finds out composite regulatory elements (combination of closely situated binding sites for distinct TFs) for predicting gene function.
Kel-Margoulis OV, Kel AE, Reuter I, Deineko IV, Wingender E. TRANSCompel: a database on composite regulatory elements in eukaryotic genes.Nucleic Acids Res. 2002 Jan 1;30(1):332-4. Pubmed PMID: 11752329; Pubmed Central PMCID:PMC99108.
2002
67
 Online tool. Needs registration.
7 PlantCARE - plant cis-acting Regulatory Element database
http://sphinx.rug.ac.be:8080/PlantCARE/		 Gives regulatory elements (represented by positional matrices), its position, sequence, core similarity, matrix similarity in the promoters of plant genes.
Magali Lescot, Patrice Dehais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouze, and Stephane Rombauts. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002 January 1; 30(1): 325-327.Pubmed Central PMCID: PMC99092
2002
76
 URL not working (as on 1 March 2013)
8 ATTED-II - Arabidopsis thaliana trans-factor and cis-element prediction database
http://www.atted.bio.titech.ac.jp		 Finds TFs and TFBS in the promoters of Arabidopsis thaliana.
Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.Nucleic Acids Res. 2007 Jan;35(Database issue):D863-9. Epub 2006 Nov 27.Pubmed PMID:17130150; Pubmed Central PMCID:PMC1716726.
2006
77
 URL not working (as on 4 March 2013)
9 YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking
http://www.yeastract.com		 Identifies potential trancriptional regulators for a given gene or potential regulons for each TF. Also, compares between DNA motifs over-represented in promoter regions of co-expressed genes and TFBS given in literature.
Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sá-Correia I.The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D446-51. Pubmed PMID: 16381908; Pubmed Central PMCID:PMC1347376.
2006
78
 Online
10 HTPSELEX
http://www.isrec.isb-sib.ch/htpselex		 Gives data from SELEX experiments for finding out specific TFBS.
Jagannathan V, Roulet E, Delorenzi M, Bucher P. HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D90-4. Pubmed PMID: 16381982; Pubmed Central PMCID: PMC1347412.
2006
81
 Limited data from SELEX experiments. Available for browsing, but querying is not possible.
11 TFSearch
http://www.cbrc.jp/research/db/TFSEARCH.html		 Finds TFBSs by searching correlated sequences vs TFMATRIX TFBS database.
Pubmed citation is not available. Other citation: Yutaka Akiyama: "TFSEARCH: Searching Transcription Factor Binding Sites", http://www.rwcp.or.jp/papia/
1995
82
 Results are displayed in a basic HTML format. Sequence should not be longer than 9999 bases. The URL http://pdap1.trc.rwcp.or.jp/research/db/TFSEARCH.html does not work any longer.
12 AlignACE
http://atlas.med.harvard.edu/cgi-bin/alignace.pl		 Identifies DNA regulatory motif.
Roth FP, Hughes JD, Estep PW, Church GM. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol. 1998 Oct;16(10):939-45. PubMed PMID: 9788350.
1998
84
 The given URL is not working. A modified approach has been incorporated into the AlignACE program and is called W-AlignACE with the URL http://www1.spms.ntu.edu.sg/~chenxin/W-AlignACE/
13 rVISTA
http://rvista.dcode.org/		 Identifies potential regulatory elements in noncoding regions of the human genome.
Loots GG, Ovcharenko I. rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21. Pubmed PMID:15215384; Pubmed Central PMCID:PMC441521
2002
85
 Online tool
14 ConSite
http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite/		 Finds TFBS, its sequence, position, strand and TFs binding to it in the promoters of higher eukaryotes.
Sandelin A, Wasserman WW, Lenhard B. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52. PubMed PMID: 15215389; PubMed Central PMCID: PMC441510.
2004
86
 Online tool
15 Proscan, Promoter Scan
http://www-bimas.cit.nih.gov/molbio/proscan/		 Finds putative pol II promoter region in eukaryotic genome with small rate of false positives.
Prestridge DS. Predicting Pol II promoter sequences using transcription factor binding sites. J Mol Biol. 1995 Jun 23;249(5):923-32. PubMed PMID: 7791218.
1995
87
 Online tool
16 DBTBS - Database of transcriptional regulation in Bacillus subtilis
http://dbtbs.hgc.jp		 Finds promoters, putative TFBS, TFs and genes regulated by them in B. subtilis. It also gives conserved hexameric motifs within upstream intergenic region of homologous genes in gram positive bacteria.
Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Yasutaro Fujita, and Kenta Nakai. DBTBS: a database of Bacillus subtilis promoters and transcription factors.Nucleic Acids Res. 2001 January 1; 29(1): 278-280. Pubmed Central PMCID: PMC29858
1999
88
 Online tool
17 ECRbase - database of Evolutionary Conserved Region
http://ecrbase.dcode.org		 Finds out evolutionary conserved region from the whole genome, promoter sequence and TFBS and includes data from human, rhesus monkey, dog, opossum, rat, mouse, chicken, frog, fugu and zebrafish. It gives positional and directional information of promoters and also the gene associated with it.
Loots G, Ovcharenko I. ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.Bioinformatics. 2007 Jan 1;23(1):122-4. Epub 2006 Nov 7. Pubmed PMID: 17090579
2006
90
 Downloadable. ECRbase ECRs corresponds to new ECRBrowser alignments. It has been updated on March 2008.
18 IMAGE
http://image.ylichron.it		 Finds putative TFBS, selects motif lengths and the number of allowed mismatches in human, mouse, D. melanogaster and yeast.
R. Casilli, A. Marongiu,S. Melchionna, P. Palazzari R. Paparcone,and V. Rosato. IMAGE: a new tool for the prediction of transcription factor binding sites.Bioinform Biol Insights. 2008; 2: 357-367. Published online 2008 October 3. Pubmed Central PMCID: PMC2735968.
2008
90
 URL not working (as on 2 March 2013)
19 Signal Scan
http://www-bimas.cit.nih.gov/molbio/signal/		 Gives signal sequences, its location, orientation, strand in the input DNA sequence of eukaryotes.
Prestridge DS. SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements. Comput Appl Biosci. 1991 Apr;7(2):203-6. PubMed PMID: 2059845.
1991
91
 Online tool
20 BPROM
http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb		 Recognizes sigma70 promoters in bacteria (mainly E. coli).
Not available in PubMed
Not available
92
 Online tool. For academic use only (as mentioned in the 'terms of use').
21 FirstEF - First Exon Finder
http://rulai.cshl.org/tools/FirstEF/		 Predicts 5' terminal exon and promoter using probabilistic models.
Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet. 2001 Dec;29(4):412-7. Erratum in: Nat Genet 2002 Nov;32(3):459. PubMed PMID: 11726928.
2001
92
 Free for non-profit institutions, commercial users need to pay a fee to obtain site license
22 Promoter 2.0 prediction Server
http://www.cbs.dtu.dk/services/Promoter/		 Predicts eukaryotic pol III promoter sequences along with position and scoring in the DNA sequences of eukaryotes.
Knudsen S. Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics. 1999 May;15(5):356-61. PubMed PMID: 10366655.
1999
92
 Free for academic users, online/downloadable
23 REDfly v3.0 - Regulatory Element Database for Drosophila
http://redfly.ccr.buffalo.edu.		 Gives the curated information about the transcriptional cis regulatory elements and modules in the metazoans.
Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.Nucleic Acids Res. 2011 Jan;39(Database issue):D118-23. doi: 10.1093/nar/gkq999. Epub 2010 Oct 21. Pubmed PMID: 20965965; Pubmed Central PMCID: PMC3013816
2010
92
 Online tool/downloadable
24 EPD - Eukaryotic Promoter Database
http://www.epd.isb-sib.ch		 It is a non-redundant database and finds out Pol II promoters and experimentally determined TSS in eukaryotes and gives frequency matrices.
Praz V, Périer R, Bonnard C, Bucher P.The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.Nucleic Acids Res. 2002 Jan 1;30(1):322-4. Pubmed PMID:11752326; Pubmed Central PMCID:PMC99099
2000
93
 Online/ Downloadable
25 OregAnno - Open Regulatory Annotation database
http://www.oreganno.org		 Gives the annotated information of regulatory regions, promoters, TFBS, haplotypes and polymorphism of vertebrates.
Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics. 2006 Mar 1;22(5):637-40. Epub 2006 Jan 5. Pubmed PMID: 16397004
2006
93
 Online. All software is licensed under the Lesser GNU Public License (LGPL). URL is not working (as on 18 April 2013)
26 PPP - Prokaryotic Promoter Prediction
http://bioinformatics.biol.rug.nl/websoftware/ppp/ppp_start.php		 Finds promoter regions and TFBS in prokaryotes. Also, finds sigma A binding sites in the upstream region.
Zomer AL, Buist G, Larsen R, Kok J, Kuipers OP. Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. J Bacteriol. 2007 Feb;189(4):1366-81. Epub 2006 Oct 6. PubMed PMID: 17028270; PubMed Central PMCID: PMC1797362.
2006
93
 Online tool. There is a login option and also shows it is licensed for using Molgen websoftware (as mentioned 'in terms of use').
27 The MAPPER2 Database
http://genome.ufl.edu/mapperdb		 Finds out binding sites in the promoter regions and in the region of initial introns and non-coding exons (since for each transcript it scans region, which extends from 10000bp upstream of transcript start to 50 bp downstream of coding sequence start) of multiple genomes in human, mouse and Drosophila genes. It includes TFs, its position in the chromosome and score. It has 3 large libraries of TFBS models (hidden markov models). The current version uses data from TRANSFAC and JASPAR.
Alberto Riva1,2,*The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites.Nucleic Acids Res. 2012 January; 40(D1): D155-D161. Published online 2011 November 24. doi: 10.1093/nar/gkr1080.Pubmed Central PMCID: PMC3245066
2011
93
 Online. Although direct access option is there but it is not directing to that page or else we have to create an account and login to it.
28 Virtual Footprint
http://www.prodoric.de/vfp/vfp_promoter.php		 Analyses individual promoters in bacterial genome and finds DNA patterns, TFBS and regulons.
Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics. 2005 Nov 15;21(22):4187-9. Epub 2005 Aug 18. PubMed PMID: 16109747.
2005
93
 Online tool
29 EP3 - Easy Promoter Prediction Program
http://bioinformatics.psb.ugent.be/webtools/ep3/		 Finds core promoter region in eukaryotes. Proved to be the best tool to find regions of transcription initiation in humans.
Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res. 2008 Feb;18(2):310-23. Epub 2007 Dec 20. PubMed PMID: 18096745; PubMed Central PMCID: PMC2203629.
2007
94
 Downloadable. Free for academic use. Requires a complete genome for the best prediction.
30 Cister - Cis element Cluster Finder
http://zlab.bu.edu/~mfrith/cister.shtml		 Predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.
Frith MC, Hansen U, Weng Z. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics. 2001 Oct;17(10):878-89. PubMed PMID: 11673232.
2001
95
 Online tool and downloadable version can be run on the command line.
31 Cluster-Buster
http://zlab.bu.edu/cluster-buster/cbust.html		 Finds clusters of pre-specified motifs with position, strand and the sequence in the promoter region.
Frith MC, Li MC, Weng Z. Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3666-8. PubMed PMID: 12824389; PubMed Central PMCID: PMC168947
2003
95
 Online tool. Also downloadable and can be run from Unix command line.
32 Eponine
http://www.sanger.ac.uk/resources/software/eponine/		 Predicts Transcription Start Site (TSS) in the genomic sequence of mammals and detects motifs.
Down TA, Hubbard TJ. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 2002 Mar;12(3):458-61. PubMed PMID: 11875034; PubMed Central PMCID: PMC155284.
2002
95
 Downloadable/ Executable. Run with Java Runtime Environment version 1.2 or later installed.
33 SCPD - Promoter Database of the yeast Saccharomyces cerevisiae
http://cgsigma.cshl.org/jian		 Finds out promoters and specific transcriptional regulatory cis elements in yeast.
Zhu J, Zhang MQ. SCPD: a promoter database of the yeast Saccharomyces cerevisiae.Bioinformatics. 1999 Jul-Aug;15(7-8):607-11. Pubmed PMID: 10487868
1999
95
 URL not working (as on 4 March 2013)
34 TSSP
http://linux1.softberry.com/berry.phtml?topic=tssp&group=programs&subgroup=promoter		 Finds the position of promoters or enhancers and TFBS in plant genome.
Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV. PlantProm: a database of plant promoter sequences. Nucleic Acids Res. 2003 Jan 1;31(1):114-7. PubMed PMID: 12519961; PubMed Central PMCID: PMC165488.
2003
95
 Online tool. For academic use only (as mentioned in the 'terms of use').
35 cisRED
http://www.cisred.org		 Finds transcriptional regulatory motif in promoter region of whole genome in mammals and other eukaryotes. Also, finds groups of similar motifs and co-occurring patterns of motifs.
Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJ.cisRED: a database system for genome-scale computational discovery of regulatory elements.Nucleic Acids Res. 2006 Jan 1;34(Database issue):D68-73. Pubmed PMID: 16381958; Pubmed Central PMCID: PMC1347438.
2005
96
 URL not working (as on 5 March 2013)
36 CpGProd - CpG Island Promoter Detection
http://pbil.univ-lyon1.fr/software/cpgprod.html		 Finds potential promoters, its orientation and CpG islands associated with it in human and mouse genome.
Ponger L, Mouchiroud D. CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics. 2002 Apr;18(4):631-3. PubMed PMID: 12016061.
2002
96
 Online/ Downloadable
37 FootPrinter
http://bio.cs.washington.edu/software		 Identifies putative regulatory elements and also conserved regions in orthologous DNA sequences.
Blanchette M, Tompa M. FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res. 2003 Jul 1;31(13):3840-2. PubMed PMID: 12824433; PubMed Central PMCID: PMC169012.
2003
96
 The URL has links to either download the tool or to open the web server. The page is redirected to another page with the latest version (this page does not open as on 9 March 2013)
38 PhyloCon - Phylogenetic Consensus for regulatory motif identification
http://ural.wustl.edu/~twang/PhyloCon/		 Identifies regulatory motifs of co-regulated genes and conserved regions among orthologous genes within a species.
Wang T, Stormo GD. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics. 2003 Dec 12;19(18):2369-80. PubMed PMID: 14668220.
2003
96
 Downloadable
39 Athena - Arabidopsis thaliana expression network analysis
http://www.bioinformatics2.wsu.edu/Athena		 Finds out promoters, TFBS and predicted CpG islands in Arabidopsis and also searches for promoters containing motifs, which are not present in the database.
O'Connor TR, Dyreson C, Wyrick JJ. Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics. 2005 Dec 15;21(24):4411-3. Epub 2005 Oct 13.Pubmed PMID:16223790.
2005
97
 Online tool. They recommend the browser mozilla firefox.
40 PAINT - Promoter Analysis and Interaction Network Toolset
http://www.dbi.tju.edu/dbi/tools/paint/		 Finds potential promoters for a given set of genes and over-represented or under-represented TFBSs on the sequences.
Vadigepalli R, Chakravarthula P, Zak DE, Schwaber JS, Gonye GE. PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification. OMICS. 2003 Fall;7(3):235-52. PubMed PMID: 14583114.
2003
97
 Online tool. Executable through 2 modules: Feasnet Builder and Feasnet Analysis and Visualization.
41 Prokaryotic promoter analysis using SAK
http://nostradamus.cs.rhul.ac.uk/~leo/sak_demo/		 Performs analysis of moderately long sequences for prokaryotic Sigma-70 promoters using Sequence Alignment Kernel method.
Gordon L, Chervonenkis AY, Gammerman AJ, Shahmuradov IA, Solovyev VV. Sequence alignment kernel for recognition of promoter regions. Bioinformatics. 2003 Oct 12;19(15):1964-71. PubMed PMID: 14555630.
2003
97
 Online tool. URL not working (as on 9 March 2013)
42 PromoterInspector
http://genomatix.gsf.de/cgi-bin/promoterinspector/promoterinspector.pl		 Predicts eukaryotic pol II promoter regions with high specificity in mammalian genomic sequences.
Scherf M, Klingenhoff A, Werner T. Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach. J Mol Biol. 2000 Mar 31;297(3):599-606. PubMed PMID: 10731414.
2003
97
 Page cannot be displayed (as on 8 March 2013)
43 ProSOM
http://bioinformatics.psb.ugent.be/software/details/ProSOM		 Predicts promoters and uses self-organizing map (SOM) to distinguish core promoter region from the rest of the genome.
Abeel T, Saeys Y, Rouzé P, Van de Peer Y. ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics. 2008 Jul 1;24(13):i24-31. PubMed PMID: 18586720; PubMed Central PMCID: PMC2718650.
2008
97
 Executable
44 SCOPE - Suite for Computational identification Of Promoter Elements
http://genie.dartmouth.edu/scope/		 Identifies pre-specified regulatory DNA motifs from the upstream sequence of the given promoter region.
Carlson JM, Chakravarty A, DeZiel CE, Gross RH. SCOPE: a web server for practical de novo motif discovery. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W259-64. Epub 2007 May 7. PubMed PMID: 17485471; PubMed Central PMCID: PMC1933170.
2007
97
 Online tool
45 CBS - Conserved Regulatory Binding sites
http://compfly.bio.ub.es/CBS		 Finds out conserved TFBS, TFs and enhancers in the promoter regions of Drosophila genomes.
Blanco E, Corominas M. CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes.BMC Genomics. 2012 Dec 10;13:688. doi: 10.1186/1471-2164-13-688. Pubmed PMID:23228284
2012
98
 Online tool/downloadable
46 CONREAL - CONserved Regulatory Elements anchored Alignment
http://conreal.niob.knaw.nl/		 Identifies conserved TFBSs (represented by PWM) between two orthologous promoter sequences.
Berezikov E, Guryev V, Plasterk RH, Cuppen E. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res. 2004 Jan;14(1):170-8. Epub 2003 Dec 12. PubMed PMID: 14672977; PubMed Central PMCID: PMC314294.
2003
98
 Online tool
47 ConTra v2
http://bioit.dmbr.ugent.be/contrav2/index.php		 Analyses TFBS in any genomic region, promoter, 5'UTR, 3'UTR region ranging from human to yeast.
Stefan Broos,Paco Hulpiau, Jeroen Galle, Bart Hooghe, Frans Van Roy, and Pieter De Bleser. ConTra v2: a tool to identify transcription factor binding sites across species, update 2011Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W74-W78. Published online 2011 May 14. doi: 10.1093/nar/gkr355. Pubmed Central PMCID: PMC3125763.
2011
98
 Online/ Downloadable
48 CpG_promoter - Human promoter mapping using CpG islands
http://rulai.cshl.org/tools/CpG_promoter/		 Maps human promoters using CpG islands.
Ioshikhes IP, Zhang MQ. Large-scale human promoter mapping using CpG islands. Nat Genet. 2000 Sep;26(1):61-3. PubMed PMID: 10973249.
2000
98
 Results are obtained through email
49 PromH(W)
http://linux1.softberry.com/berry.phtml?topic=promhw&group=programs&subgroup=promoter		 Identifies promoters with accurate TSS position in orthologous pairs of genes.
Solovyev VV, Shahmuradov IA. PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3540-5. PubMed PMID: 12824362; PubMed Central PMCID: PMC168932.
2003
98
 For academic use only
50 PromoSer
http://biowulf.bu.edu/zlab/PromoSer/		 Extracts region around TSS specified by the user and also shows repeats if specified for human, mouse and rat genes.
Halees AS, Leyfer D, Weng Z. PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res. 2003 Jul 1;31(13):3554-9. PubMed PMID: 12824364; PubMed Central PMCID: PMC168956.
2003
98
 Online tool/ Downloadable
51 PromScan
http://molbiol-tools.ca/promscan/		 Scans potential sigma 54-RNAP-binding sites or any ungapped motif in the given DNA sequence.
Not available in PubMed
Not available
98
 Online tool
52 PSPA - Position Specific Propensity Analysis
http://cagr.pcbi.upenn.edu/PSPA/		 Predicts core promoters and also reports if there are any CpG islands in humans.
Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res. 2007;35(10):3203-13. Epub 2007 Apr 22. PubMed PMID: 17452354
2007
98
 Online tool
53 Tfsitescan
http://www.ifti.org/cgi-bin/ifti/Tfsitescan.pl		 Performs promoter sequence analysis.
Not available in PubMed
Not available
98
 Online tool. Input promoter sequences should be approximately 500 nucleotides.
54 ABS
http://genome.imim.es/datasets/abs2005/index.html		 It is a manually curated database used to find out TFBS in the promoter regions of orthologous vertebrate genes. Also, predicts promoters for the specified TFs.
Enrique Blanco,1,2,* Domenec Farre,1,2 M. Mar Alba,1 Xavier Messeguer,2 and Roderic Guigo1. ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. Nucleic Acids Res. 2006 January 1; 34(Database issue): D63-D67.Published online 2005 December 28. doi: 10.1093/nar/gkj116.Pubmed Central PMCID: PMC1347478.
2005
99
 Online/ Downloadable.
55 Ceres
http://bioinformatics1.smb.wsu.edu/Ceres		 Finds out overrepresented TFBS and nucleosome position in the promoter sequences of yeast genome.
Morris RT, O'Connor TR, Wyrick JJ. Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae.Bioinformatics. 2010 Jan 15;26(2):168-74. doi: 10.1093/bioinformatics/btp657. Epub 2009 Dec 2. Pubmed PMID: 19959498.
2009
99
 Online tool. They recommend the browser mozilla firefox.
56 CpGIF - CpG Island Finder
http://people.usd.edu/~sye/cpgisland/CpGIF.htm		 Finds CpG islands in DNA sequences.
Sujuan Y, Asaithambi A, Liu Y. CpGIF: an algorithm for the identification of CpG islands. Bioinformation. 2008 May 20;2(8):335-8. PubMed PMID: 18685720; PubMed Central PMCID: PMC2478732.
2008
99
 Page cannot be found (as on 11 March 2013) but directs to another page, which needs USD username and password.
57 DBTGR - Database of Tunicate Gene Regulation
http://dbtgr.hgc.jp		 Gives regulatory information of tunicate genes about promoter length, putative TFBS, associated factors, location of the gene expression and also compares the promoters of homologous genes in different species to find out conserved cis elements.
Sierro N, Kusakabe T, Park KJ, Yamashita R, Kinoshita K, Nakai K. DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D552-5. Pubmed PMID:16381930; Pubmed Central PMCID:PMC1347427
2005
99
 Online tool
58 DragonGSF - Dragon gene start finder
http://sdmc.lit.org.sg/promoter/dragonGSF1_0/genestart.htm		 Gives information on CpG islands, TSS location and downstream region of TSS in mammalian genomes.
Bajic VB, Seah SH. Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res. 2003 Aug;13(8):1923-9. Epub 2003 Jul 17. PubMed PMID: 12869582; PubMed Central PMCID: PMC403784.
2003
99
 Page cannot be displayed (as on 11 March 2013)
59 DragonPF - Dragon Promoter Finder
http://research.i2r.a-star.edu.sg/promoter/promoter1_5/DPF.htm%20Or%20http://sdmc.krdl.org.sg:8080/promoter/		 Predicts TSS position in RNA pol II promoters of vertebrates.
Bajic VB, Seah SH, Chong A, Zhang G, Koh JL, Brusic V. Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics. 2002 Jan;18(1):198-9. PubMed PMID: 11836231.
2002
99
 Page cannot be displayed (as on 9 March 2013)
60 FindTerm
http://linux1.softberry.com/berry.phtml?topic=findterm&group=programs&subgroup=gfindb		 Finds terminators in bacterial genomes.
Not available in PubMed
Not available
99
 Online tool. For academic use only (as mentioned in the 'terms of use').
61 FPROM
http://linux1.softberry.com/berry.phtml?topic=fprom&group=programs&subgroup=promoter		 Predicts potential transcription start positions.
Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL. Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol. 2006;7 Suppl 1:S3.1-13. Epub 2006 Aug 7. Review. PubMed PMID: 16925837; PubMed Central PMCID: PMC1810552.
2006
99
 Online tool. For academic use only (as mentioned in the 'terms of use').
62 GPMiner
http://GPMiner.mbc.nctu.edu.tw/		 Identifies TSSs and regulatory features (TFBS, CpG islands, tandem repeats, the TATA box, the CCAAT box, the GC box, over-represented oligonucleotides, DNA stability and GC-content) in a promoter sequence, and finds co-occurrence of cis-regulatory elements in co-expressed genes using a novel system.
Lee TY, Chang WC, Hsu JB, Chang TH, Shien DM. GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. BMC Genomics. 2012;13 Suppl 1:S3. doi: 10.1186/1471-2164-13-S1-S3. Epub 2012 Jan 17. Pubmed PMID:22369687; Pubmed Central PMCID:PMC3587379.
2012
99
 Online tool
63 jPREdictor
http://bibiserv.techfak.uni-bielefeld.de/jpredictor/		 Predicts cis-regulatory elements and is based on combining individual motifs into pair or higher order motifs with minimal and maximal distance.
Fiedler T, Rehmsmeier M. jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W546-50. PubMed PMID: 16845067; PubMed Central PMCID: PMC1538890.
2006
99
 Online tool/Downloadable. Version 1.23 of jPREdictor is available since April 2008.
64 Marfinder
http://genomecluster.secs.oakland.edu/marwiz/		 Predicts the occurrence of Matrix Association Regions or MARs.
Rogozin IB, Glazko GV, Glazkov MV. Computer prediction of sites associated with various elements of the nuclear matrix. Brief Bioinform. 2000 Feb;1(1):33-44. PubMed PMID: 11466972.
2000
99
 Online tool
65 POXO
http://www.bioinfo.biocenter.helsinki.fi/poxo		 Contains different tools to find out overrepresented and underepresented TFBS, different regulatory regions and also to retrieve upstream sequences from the co-expressed genes of Arabidopsis thaliana.
Kankainen M, Pehkonen P, Rosenstöm P, Törönen P, Wong G, Holm LPOXO: a web-enabled tool series to discover transcription factor binding sites.Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W534-40. Pubmed PMID:16845065; Pubmed Central PMCID:PMC1538773.
2006
99
 Online tool. Results may be stored at random time and may be removed without notice to users.
66 ppdb - plant promoter database
http://www.ppdb.gene.nagoya-u.ac.jp		 Finds core promoter structure, TSS, regulatory elements in Arabidopsis and rice.
Yamamoto YY, Obokata J. ppdb: a plant promoter database. Nucleic Acids Res. 2008 Jan;36(Database issue):D977-81. Epub 2007 Oct 18. Pubmed PMID:17947329; Pubmed Central PMCID: PMC2238996.
2007
99
 URL not working (as on 4 March 2013)
67 STIFDB2 - Stress Responsive Transcription Factor Database
http://caps.ncbs.res.in/stifdb2		 Finds out abiotic stress responsive genes (upregulated), TF, TFBS of Arabidopsis, Oryza sativa subsp. japonica and Oryza sativa subsp. indica and provides 1000bp promoter region along with 5' UTR to find out TFBS bound by abiotic stress responsive TF.
Naika M, Shameer K, Mathew OK, Gowda R, Sowdhamini R. STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice.Plant Cell Physiol. 2013 Feb;54(2):e8. doi: 10.1093/pcp/pcs185. Epub 2013 Jan 10. Pubmed PMID: 23314754; Pubmed Central PMCID: PMC3583027.
2009
99
 Online tool/downloadable
68 TRRD - Transcription Regulatory Regions Database
http://www.bionet.nsc.ru/trrd/		 Contains data on location and functions of transcriptional regulatory regions and gene expression patterns of eukaryotic genes.
Kolchanov NA, Ignatieva EV, Ananko EA, Podkolodnaya OA, Stepanenko IL, Merkulova TI, Pozdnyakov MA, Podkolodny NL, Naumochkin AN, Romashchenko AG. Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res. 2002 Jan 1;30(1):312-7.Pubmed PMID:11752324; Pubmed Central PMCID:PMC99088
2002
99
 Online tool. TRRD Release 7.0 on-line (TRRDSTARTS): September 2005. Its access can be through SRS. All the information is arranged into different sub-tools. Only confirmed experimental information is included in TRRD.
69 TSSG
http://linux1.softberry.com/berry.phtml?topic=tssg&group=programs&subgroup=promoter		 Recognizes human pol II promoter region and transcription start site.
Solovyev V, Salamov A. The Gene-Finder computer tools for analysis of human and model organisms genome sequences. Proc Int Conf Intell Syst Mol Biol. 1997;5:294-302. PubMed PMID: 9322052
1997
99
 Online tool. For academic use only (as mentioned in the 'terms of use').
70 WEBGENE
http://www.itb.cnr.it/sun/webgene/		 Predicts and performs analysis of protein-coding gene structures (Software suite).
Milanesi L, D'Angelo D, Rogozin IB. GeneBuilder: interactive in silico prediction of gene structure. Bioinformatics. 1999 Jul-Aug;15(7-8):612-21. PubMed PMID: 10487869.
1999
99
 Online tool
71 angaGEDUCI - Anopheles gambiae Gene Expression Database at UC Irvine
http://www.angaged.bio.uci.edu		 Finds out expression of genes in different stages, tissue, pattern of interest and also finds the conserved promoter sequence motif, which is important for regulation.
Dissanayake SN, Marinotti O, Ribeiro JM, James AA. angaGEDUCI: Anopheles gambiae gene expression database with integrated comparative algorithms for identifying conserved DNA motifs in promoter sequences. BMC Genomics. 2006 May 17;7:116. Pubmed PMID: 16707020; Pubmed Central PMCID: PMC1524951.
2006
100
 Online/downloadable.
72 Bayes Aligner
http://ccmbweb.ccv.brown.edu/cgi-bin/bayes_align12.pl		 Performs phylogenetic footprinting.
Zhu J, Liu JS, Lawrence CE. Bayesian adaptive sequence alignment algorithms. Bioinformatics. 1998;14(1):25-39. PubMed PMID: 9520499.
1998
100
 Online tool. Total maximum sequence length (query sequence + comparison sequence) is restricted to 4000. To run moltiple sequence, download it.
73 ConCisE Scanner - Conserved Cis element Scanner
http://concise-scanner.cchmc.org/concise-scanner/index.jsp		 Searches for genome-wide ortholog conserved Cis-elements.
Jegga AG, Chen J, Gowrisankar S, Deshmukh MA, Gudivada R, Kong S, Kaimal V, Aronow BJ. GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs. Nucleic Acids Res. 2007 Jan;35(Database issue):D116-21. Epub 2006 Dec 18. PubMed PMID: 17178752; PubMed Central PMCID: PMC1781107.
2006
100
 Online tool
74 CONFAC - Conserved Transcription Factor Binding Site Finder
http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl		 Identifies conserved TFBS in the promoter regions of human and corresponding mouse homolog.The software compares non-coding regulatory sequences between human and mouse genomes to identify conserved TFBSs that are significantly more common in promoters of groups of genes of interest from microarray analyses than in a set of unchanging control genes.
Karanam S, Moreno CS. CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets.Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W475-84. Pubmed PMID:15215433; Pubmed Central PMCID:PMC441491
2004
100
 Downloadable. Confac website cannot be viewed with Netscape Navigator v4.7.
75 CONPRO - CONsensus PROmoter
http://stl.bioinformatics.med.umich.edu/conpro		 Predicts highly specific promoters in human genes.
Liu R, States DJ. Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. Genome Res. 2002 Mar;12(3):462-9. PubMed PMID: 11875035; PubMed Central PMCID: PMC155291.
2002
100
 Page cannot be displayed (as on 11 March 2013)
76 CorePromoter - Core Promoter Prediction Program
http://rulai.cshl.org/tools/genefinder/CPROMOTER/index.htm		 Predicts putative TSS and core promoter in humans.
Zhang MQ. Identification of human gene core promoters in silico. Genome Res. 1998 Mar;8(3):319-26. PubMed PMID: 9521935; PubMed Central PMCID: PMC310696.
1998
100
 Online tool. Free for non-profit institutions for non-commercial purposes. Commercial users need site license.
77 COTRASIF
http://biomed.org.ua/COTRASIF/		 Finds out the conserved TFBS motif sequences and compare the results with the existing TFBS in higher eukaryotes.To decrease FP that occur by chance, it will predict only those TFBS, which are also found in the promoters of orthologous genes of related species.
Tokovenko B, Golda R, Protas O, Obolenskaya M, El'skaya A. COTRASIF: conservation-aided transcription-factor-binding site finder.Nucleic Acids Res. 2009 Apr;37(7):e49. doi: 10.1093/nar/gkp084. Epub 2009 Mar 5. Pubmed PMID: 19264796; Pubmed Central PMCID:PMC2673430.
2009
100
 Online tool. Results are sent through email. Free for non-commercial use. Commercial users need license.
78 cREMaG - cis Regulatory Elements in Mammalian Genome
http://www.cremag.org.		 Finds out overrepresented cis regulatory elements and TFs in the promoter region of co-regulated mammalian genes and also gives alternative TSS and CpG islands information.
Piechota M, Korostynski M, Przewlocki R. Identification of cis-regulatory elements in the mammalian genome: the cREMaG database. PLoS One. 2010 Aug 31;5(8):e12465. doi: 10.1371/journal.pone.0012465. Pubmed PMID:20824209; Pubmed Central PMCID:PMC2930848.
2010
100
 Online tool.
79 DistanceScan
https://www.omnifung.hki-jena.de/Rpad/Distance_Scan/index.htm		 Finds out overrepresented pairs of TFBS in the promoter regions of higher eukaryotes.
Shelest V, Albrecht D, Shelest E. DistanceScan: a tool for promoter modeling. Bioinformatics. 2010 Jun 1;26(11):1460-2. doi: 10.1093/bioinformatics/btq132. Epub 2010 Mar 25. Pubmed PMID:20360058.
2009
100
 Page opens but a message displayed- 'untrusted connection'.
80 DoOPSearch
http://doopsearch.abc.hu		 Finds out similar conserved motifs in the promoter regions of plant and chordate genes.
Endre Sebestyén, Tibor Nagy, Sándor Suhai, and Endre Barta. DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes.BMC Bioinformatics. 2009; 10(Suppl 6): S6. Published online 2009 June 16. doi: 10.1186/1471-2105-10-S6-S6. Pubmed Central PMCID: PMC2697653.
2009
100
 Licensed and downloadable.
81 EnsemPro - Ensemble Promoter
URL not available		 Predicts promoters.
Won HH, Kim MJ, Kim S, Kim JW. EnsemPro: an ensemble approach to predicting transcription start sites in human genomic DNA sequences. Genomics. 2008 Mar;91(3):259-66. PubMed PMID: 18164178.
2008
100
 URL is not available (as on 11 March 2013)
82 FGENEH
http://www.bioscience.org/urllists/genefind.htm		 Predicts exon in human gene sequences.
Solovyev VV, Salamov AA, Lawrence CB. Identification of human gene structure using linear discriminant functions and dynamic programming. Proc Int Conf Intell Syst Mol Biol. 1995;3:367-75. PubMed PMID: 7584460.
1995
100
 Page cannot be found (as on 11 March 2013). Even though the page shows error, search option is there.
83 FunSiteP
http://transfac.gbf.de/dbsearch/funsitep/fsp.html		 Identifies promoters and its functional class.
Kondrakhin YV, Kel AE, Kolchanov NA, Romashchenko AG, Milanesi L.Eukaryotic promoter recognition by binding sites for transcription factors.Comput Appl Biosci. 1995 Oct;11(5):477-88.PMID: 8590170
1995
100
 Server not found (as on 12 March 2013)
84 GrailEXP - Grail Experimental Gene Discovery Suite
http://compbio.ornl.gov/Grail-1.3/		 Predicts exons, genes, promoters, poly As, CpG islands, EST similarities, and repetitive elements within DNA sequence.
Uberbacher EC, Hyatt D, Shah M. GrailEXP and Genome Analysis Pipeline for genome annotation. Curr Protoc Bioinformatics. 2004 Feb;Chapter 4:Unit4.9. PubMed PMID: 18428726.
2004
100
 The given URL is not working. Another link is given in the same page which directs to the homepage. Downloadable tool.
85 HemoPDB - Hematopoiesis Promoter Database
http://bioinformatics.med.ohio-state.edu/HemoPDB		 Finds out promoters, TFs, target genes and genes expressed for particular cell type.
Twyla T. Pohar, Hao Sun, and Ramana V. Davuluri* HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. Nucleic Acids Res. 2004 January 1; 32(Database issue): D86-D90.doi: 10.1093/nar/gkh056. Pubmed Central PMCID: PMC308790
2004
100
 URL not working (as on 1 March 2013)
86 INCLUSive
http://tomcatbackup.esat.kuleuven.be/inclusive/		 Performs analysis of gene expression data and finds cis-regulatory sequence elements.
Coessens B, Thijs G, Aerts S, Marchal K, De Smet F, Engelen K, Glenisson P, Moreau Y, Mathys J, De Moor B. INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3468-70. PubMed PMID: 12824346; PubMed Central PMCID: PMC169021.
2003
100
 Downloadable.
87 McPromoter - The Markov Chain Promoter Prediction Server
http://tools.igsp.duke.edu/generegulation/McPromoterMMII/		 Locates eukaryotic RNA polymerase II transcription start sites. Also, includes models for vertebrates or D. melanogaster DNA.
Ohler U. Promoter prediction on a genomic scale--the Adh experience. Genome Res. 2000 Apr;10(4):539-42. PubMed PMID: 10779494; PubMed Central PMCID: PMC310866.
2000
100
 Free for non-commercial users and results are obtained through email. The version has been upadated for Drosophila sequences in 2006.
88 MEDUSA - Motif Element Detection Using Sequence Agglomeration
http://cbio.mskcc.org/leslielab/software/medusa		 Predicts expressions of target genes by identifying regulators, motifs and promoters. It also gives information about heme and oxygen regulatory network in yeast.
Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C. Learning regulatory programs that accurately predict differential expression with MEDUSA. Ann N Y Acad Sci. 2007 Dec;1115:178-202. Epub 2007 Oct 12. PubMed PMID: 17934055.
2007
100
 Implemented in MATLAB and is free for academic usage. Downloadable.
89 Melina II
http://melina2.hgc.jp/public/index.html		 Predicts potential DNA motifs using a combination of five programs and compares the results graphically. Also, similar motifs can be found by giving weight matrix from predicted motifs to upstream sequences of human, mouse, yeast, E.coli and A. thaliana.
Okumura T, Makiguchi H, Makita Y, Yamashita R, Nakai K. Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W227-31. Epub 2007 May 30. PubMed PMID: 17537821; PubMed Central PMCID: PMC1933176.
2007
100
 Online tool. Flash Plug-in must be installed (if not installed earlier). Also, it has been mentioned to try once on a computer without flash plug-in.
90 MetaProm
URL not available		 Recognizes promoter region and its correlation with CpG islands.
Wang J, Ungar LH, Tseng H, Hannenhalli S. MetaProm: a neural network basedmeta-predictor for alternative human promoter prediction. BMC Genomics. 2007 Oct 17;8:374. PubMed PMID: 17941982; PubMed Central PMCID: PMC2194789.
2007
100
 URL is not available (as on 11 March 2013)
91 MotifLab
http://www.motiflab.org		 Finds TFBS and cis regulatory modules in the regulatory region of the genome.
Klepper K, Drablřs F. MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.BMC Bioinformatics. 2013 Jan 16;14:9. doi: 10.1186/1471-2105-14-9. Pubmed PMID: 23323883; Pubmed Central PMCID:PMC3556059.
2013
100
 Downloadable.
92 PatSearch
http://bighost.area.ba.cnr.it/BIG/PatSearch/		 Finds combinations of oligonucleotide consensus sequences, secondary structure elements and position weight matrices.
Grillo G, Licciulli F, Liuni S, Sbisŕ E, Pesole G. PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences.Nucleic Acids Res. 2003 Jul 1;31(13):3608-12.PMID: 12824377
2000
100
 Page cannot be found (as on 12 March 2013)
93 PePPER - Prokaryote Promoter Prediction
http://pepper.molgenrug.nl/index.php/pepper-tools/promoter-predictie-tool		 Predicts promoters for prokaryotes based on curated PWM and HMM models. Also, analyses regulons, TFBS and also in addition includes new L. lactis regulon database.
de Jong A, Pietersma H, Cordes M, Kuipers OP, Kok J. PePPER: a webserver for prediction of prokaryote promoter elements and regulons. BMC Genomics. 2012 Jul 2;13:299. doi: 10.1186/1471-2164-13-299. PMID: 22747501
2012
100
 Online tool
94 PRECISE - Prediction of REgulatory CIS-acting Elements
http://www.dpw.wau.nl/pv/pub/precise/		 Predicts regulatory cis acting elements in Arabidopsis.
Trindade LM, van Berloo R, Fiers M, Visser RG. PRECISE: software for prediction of cis-acting regulatory elements. J Hered. 2005 Sep-Oct;96(5):618-22. Epub 2005 Aug 31. PubMed PMID: 16135709.
2005
100
 Page cannot be displayed (as on 12 March 2013)
95 ProGA - Eukaryotic Promoters Recognition by Genetic Algorithm
http://wwwmgs.bionet.nsc.ru/mgs/programs/proga/		 Recognizes eukaryotic promoters.
Not available in PubMed
Not available
100
 Online tool but the output shows error.
96 PromAn
http://bips.u-strasbg.fr/PromAn/
Lardenois A, Chalmel F, Bianchetti L, Sahel JA, Léveillard T, Poch O. PromAn: an integrated knowledge-based web server dedicated to promoter analysis. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W578-83. PubMed PMID: 16845074; PubMed Central PMCID: PMC1538850.
2006
100
 Tool has been discontinued
97 PromExtra - Human Promoter Extractor
http://www.biorainbow.com/promextra/index.php		 Extracts promoters for a given list of human genes.
Not available in PubMed
Not available
100
 Downloadable
98 PromFD 1.0
URL not available		 Recognizes vertebrate RNA polymerase II promoters and location of TATA box. Also, finds significant matrices in the promoters.
Chen QK, Hertz GZ, Stormo GD. PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput Appl Biosci. 1997 Feb;13(1):29-35. PubMed PMID: 9088706.
1997
100
 URL is not available (as on 12 March 2013)
99 PromFind
http://biowaredb.org/site/index.php?Itemid=31&id=4775&option=com_content&task=view
Not available in PubMed
Not available
100
 Server error (as on 12 March 2013)
100 PromH(G)
http://linux1.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promoter		 Predicts promoters, position of TATA box and TFBS using orthologous sequences.
Solovyev VV, Shahmuradov IA. PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3540-5. PubMed PMID: 12824362
2003
100
 Online tool. For academic use only (as mentioned in the 'terms of use').
101 PROMOCO - PROfile Motif Collection
URL not available		 Finds all conserved motifs in the given promoter sequence.
Li G, Lu J, Olman V, Xu Y. Prediction of cis-regulatory elements: from high-information content analysis to motif identification. J Bioinform Comput Biol. 2007 Aug;5(4):817-38. PubMed PMID: 17787058.
2007
100
 URL is not available (as on 12 March 2013)
102 SiTaR - Site Tracking and Recognition
http://sbi.hki-jena.de/sitar/index.php		 Finds TFBS and reduces FP predictions.
Fazius E, Shelest V, Shelest E. SiTaR: a novel tool for transcription factor binding site prediction.Bioinformatics. 2011 Oct 15;27(20):2806-11. doi: 10.1093/bioinformatics/btr492. Epub 2011 Sep 4. Pubmed PMID:21893518
2011
100
 URL not working (as on 2 March 2013)
103 TFExplorer
http://mars.kribb.re.kr:8080/tfExplorer/		 Gives information about TFBS in the promoter region and the phylogenetic footprinting. It also gives the names of genes based on the sequence pattern in the promoters.
Kim J, Seo J, Lee YS, Kim S. TFExplorer: integrated analysis database for predicted transcription regulatory elements. Bioinformatics. 2005 Feb 15;21(4):548-50. Epub 2004 Oct 5. Pubmed PMID:15466909.
2004
100
 URL not working (as on 1 March 2013)
104 TrFAST - Transcription Factor Search and Analysis Tool
http://www.fi-pk.com/trfast.html		 Finds out consensus sequence of TFBS, which specifically bind to the regulatory region of gene involved in signalling pathway and gives the list of bound TFs.
Seemab U, Ain Qu, Nawaz MS, Saeed Z, Rashid S.TrFAST: a tool to predict signaling pathway-specific transcription factor binding sites.Genomics Proteomics Bioinformatics. 2012 Dec;10(6):354-9. doi: 10.1016/j.gpb.2012.06.007. Epub 2012 Dec 2.PMID: 23317703
2012
100
 The website in 2012 abstract links to introduction page and it didn't provide any search option.
105 TSSW
http://linux1.softberry.com/berry.phtml?topic=tssw&group=programs&subgroup=promoter		 Recognizes human pol II promoter region and start of transcription.
Solovyev V, Salamov A. The Gene-Finder computer tools for analysis of human and model organisms genome sequences. Proc Int Conf Intell Syst Mol Biol. 1997;5:294-302. PubMed PMID: 9322052.
1997
100
 Online tool. For academic use only (as mentioned in the 'terms of use').
copyright © Dr. Kshitish Acharya K; all rights reserved

real time tracking