PMBL - DATABASES - SEQUENCIES - NUCLEIC ACIDS

• HCtata - TATA Signaling Prediction (Hamming Clustering Method) - WebGene Server (Italy)
• MatInspector - Search Sequence for Transcription Factor Binding Sites - GSF (Germany)
• McPromoter - Prediction of Transcription Start Sites in Eukaryotic DNA - Univ Erlangen (Germany)
• NNPP - Promoter Prediction - LBNL Human Genome Center (US)
• Recognition of PolII Promoter Region & Transcription Start Signals Using
• TSSG (BCM Gene Finder) - promoter.dat TFD Subset - BCM (US)
• TSSW (BCM Gene Finder) - TRANSFAC Database - BCM (US)
• Signal Scan - Search Search for Eukaryotic Transcriptional Elements - BIMAS (US)
• Target Finder - Search for target genes of DNA-binding proteins - TigemNet (Italy)
• TESS - Transcription Factor Binding Site Sequence Search - U Penn (US)
• Tfsitescan - Promoter analysis - MIRAGE -IFTI (US)

Gibbs Motif Sampler Homepage (E.C. Rouchka and B. Thompson, Bioinformatics Laboratory of  Wadsworth Center, U.S.A.) - I have linked to the prokaryotic DNA default setting page. On the next page I have presented data the IHF-binding site (consensus: WWWTCAA[N4]TTR).

RSA-tools - Gibbs (A. Neuwald & Jacques van Helden, Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, Belgium) - type in the matrix size desired and deselect "add reverse complement strand."  After running the program once I would delete those sequences from the discovery set which align imperfectly.

 BindGene (C. Lockwood, University of Manchester, United Kingdom) - I have found this site particularly useful.  If your sequence is less than 2kb use the default settings.  If you paste 10kb of data, I suggest changing the "shuffled matrices" to "0."

 TESS - String Search Page (Center for Bioinformatics, University of Pennsylvania, U.S.A.) - this site requires that one enter the motif consensus sequence (Search My Site Strings), and is limited to 2000 nt per search. N.B. This site also permits searching TRANSFAC Strings. Choose "small Javal applets" to view the results of the search.

Create Matrix File (J. Zheng, Queen's University, Canada) - creates a matrix from a DNA Clustal alignment and also presents the consensus:

DNA Motifs Gibbs Sampler - SeSiMCMC - the Sequence Similarities by Markov Chain Monte-Carlo algorithm finds DNA motifs of unknown length and complicated structure in a set of unaligned DNA sequences. It uses an improved motif length estimator and careful Bayesian analysis of the possibility of a site absence in a sequence. Reference: A.V. Favorov et al.. 2005.  Bioinformatics 21: 2240-2245.

PromScan (D.J. Studholme & R. Dixon. 2003. Domain architectures of sigma54-dependent transcriptional activators. J. Bacteriol. 185:1757-67; as modified by S. Richards, Queen's University, Canada). Scans small genomes for potential factor-binding sites including IHF-binding sites. If a *.ptt file is included the results will indicate the position of the promoter relative to the nearest gene.

FindTerm (Softberry Inc.) - currently the only tool on the internet for mapping rho-independent terminators. You might consider using the advanced feature options and minimally increase the default energy threshold to -12.0.

TransTerm (Michael Nuhn, Nano+Bio-Center) - TransTerm searches for rho-independent terminators in the vicinity of annotated genes. This TIGR program can be accessed online in two ways. If you have the genome in GenBank format to use this program since it will only look for terminators in the vicinity of the annotated genes. If the genome has not been annotated use this site. The latter site combines Glimmer and RBSfinder with TransTerm.

Tools to find motif clusters in DNA sequences - one should probably start at ZLAB (Dr. Zhiping Weng, Boston University, U.S.A) which has developed a  wide range of tools to interaction between regulatory proteins and their DNA/RNA target sites including:

 Cluster-Buster
 Comet
 Cister

Find short split motifs in DNA sequences with YMF (Reference: Sinha, S. & Tompa, M. 2002. Nucleic Acids Research
Motif Sampler - tries to find over-represented motifs (cis-acting regulatory elements) in the upstream region of a set of co- regulated genes. This motif finding algorithm uses Gibbs sampling to find the position probability matrix that represents the motif. Be sure to "uncheck" the appropriate box if you don't want the complementary strand included in the analysis. (Reference: G. Thijs et al. 2002. J. Comput. Biol. 9: 447-464.)
Melina - Motif Elucidator in Nucleotide Sequence Assembly (Human Genome Center, University of Tokyo, Japan) - helps one extract a set of common motifs shared by functionally-related DNA sequences. It  utilizes CONSENSUS, GIBBS DNA, MEME and Coresearch  which are considered to be the most progressive motif search algorithms. Each algorithms is supplied with an impressive set of selection parameters. 

BioProspector  Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes (Stanford University AI Lab, U.S.A.) - uses a Gibbs sampling strategy to examine the upstream region of genes in the same gene expression pattern group and looks for regulatory sequence motifs. BioProspector uses Markov background to model the base dependencies of non-motif bases, which greatly improved the specificity of the reported motifs.
BioOptimizer - is an algorithm designed to clean up the motifs found by BioProspector, Consensus, AlignACE & MEME by finding the configuration of motif start sites that maximizes a scoring function (Reference: S.T. Jensen & J.S. Liu 2004 Bioinformatics 20:1557-1564).

PROMOTERS & TERMINATORS

B. Eukaryotic

Not being a eukaryotic molecular biologist I cannot comment on utility and accuracy of the following promoter- prediction programs. You might want to visit The Eukaryotic Promoter Database and download their organism-specific promoter databases to test the following.  

Neural Network Promoter Prediction (Berkeley Drosophila Genome Project, U.S.A.) (Reference: M.G. Reese 2001. Comput. Chem. 26: 51-6).
Promoter 2.0 Prediction Server (S. Knudsen,Center for Biological Sequence Analysis, Technical University of Denmark) - predicts transcription start sites of vertebrate Pol II promoters in DNA sequences
PROMOSER - Human, Mouse and Rat promoter extraction service (Boston University, U.S.A.) - maps promoter sequences and transcription start sites in mammalian genomes. (Reference: S. Anason et al. 2003. Nucl. Acids. Res. 2003 31: 3554-59).
Dragon Gene Start Finder (Institute for Infocomm Research, Singapore)
Promoter and gene expression regulatory motifs search (Softberry, U.S.A.) - offers a variety of promoter- scanning prrograms  

C. Transcriptional terminators

TransTerm (Michael Nuhn, Nano+Bio-Center) - TransTerm searches for rho-independent terminators in the vicinity of annotated genes. This TIGR program can be accessed online in two ways. If you have the genome in GenBank format to use this program since it will only look for terminators in the vicinity of the annotated genes. If the genome has not been annotated use this site. The latter site combines Glimmer and RBSfinder with TransTerm.

FindTerm (Softberry Inc.) - can also be used for mapping rho-independent terminators. You might consider using the advanced feature options and minimally increase the default energy threshold to -12.0. Please note that the online version of this program will only find one terminator at a time.  If you are dealing with a long sequence, once you have located a terminator, delete it from the DNA sequence and resubmit.

RibEx: Riboswitch Explorer - scans <40kb DNA for potential genes (which are linked to BLASTP) and several hundred regulatory elements, including riboswitches. If you click on the "search for attenuators" it finds terminators and antiterminators. (Reference: C. Abreu-Goodger & E. Merino. 2005. Nucl. Acids Res. 33: W690-W692).

ABS Blanco E.^1,2, Farre D.^1,2, Alba M.¹, Messeguer X.² and Guigo R.¹
Experimentally verified orthologous transcription factor binding sites
database       summary

ACTIVITY
Functional DNA/RNA site activity
database       summary

AGRIS - Arabidopsis Gene Regulatory Informmation Server Davuluri RV¹, Sun H¹, Palaniswamy SK¹, Matthews N², Molina C², Grotewold E²
Arabidopsis promoters, transcription factors and their target genes
database       summary

TRANSFAC^® Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A.E., and Wingender, E.
Transcription factors, gene regulation, positional weight matrices
database       summary

ASPD Valuev, V.P., Afonnikov D.A., Ponomarenko M.P., Kolchanov N.A.
Artificial Selected Proteins/Peptides Database
database       summary

cisRED Robertson A.G.¹, Bilenky M.¹, Lin K.¹, He A.¹, Yuen, W.¹, Dagpinar M.¹, Varhol R.¹, Teague K.¹, Griffith O.L.¹, Zhang X.¹, Pan, Y.¹, Hassel M.¹, Sleumer M.C.¹, Pan, W.¹, Pleasance E.D.¹, Chuang, M.¹, Hao H.¹, Li Y.Y.¹, Robertson N.¹, Fjell C.¹, Li B.¹, Montgomery S.B.¹, Astakhova T.¹, Zhou J.², Sander J.², Siddiqui A.S.¹ and Jones S.J.M.¹
Phylogenetically conserved regulatory DNA sequence motifs
database       summary

 DBD Kummerfeld S.K. and Teichmann S.A.
Transcription factor prediction database
database       summary

 DBTSS Yamashita R.¹, Suzuki, Y.², Wakakguri, H.², Nakai, K.¹, Sugano, S.²
Database of transcriptional start sites
database       summary

 DoOP - Databases of Orthologous Promoters Barta E.¹, Sebestyén E.¹, Pálfy T.B.¹, Tóth G.¹, Ortutay C.P.¹ and Patthy L.2
Clusters of orthologous upstream sequences from chordates and plants
 

 EPD Cavin Périer, R.¹, Praz, V.², Bucher, P.²
Eukaryotic POL II promoters with experimentally-determined transcription start sites
database       summary

GeneNet Ananko, E.A., Podkolodny, N.L., Stepanenko, I.L., Podkolodnaya, O.A., Rasskazov, D.A., Miginsky, D.S., Likhoshvai, V.A., Ratushny, A.V., Podkolodnaya, N.N., Kolchanov, N.A.
Database on gene network components
database       summary

 HTPSELEX
Transcription factor binding site sequences obtained using high-throughput SELEX method
database       summary

 JASPAR
Collection of PSSMs for transcription factor DNA-binding sites
database       summary

 MAPPER
Putative transcription factor binding sites in various genomes
database       summary

 ooTFD Ghosh D.
Transcription factors and gene expression
database       summary

 PLACE Higo, K.
Plant cis-acting regulatory elements
database       summary

PlantCARE Rombauts, S.¹, Bonnet, E.¹, Thijs, G.³, Marchal, K.³, Moreau, Y.³, Van de Peer, Y.¹, Rouze, P.²
Plant cis-acting regulatory elements
database       summary

 PlantProm
Plant promoter sequences
database       summary

rSNP Guide
Single nucleotide polymorphisms in regulatory gene regions
database       summary

 SELEXdb
Selected DNA/RNA functional site sequences
database       summary

 SKY/M-FISH and CGH
Fluorescent images of chromosomes and cytogenetic data
database       summary

 SwissRegulon Pachkov M., Erb I., Molina N. and van Nimwegen E.
Genome-wide annotations of regulatory sites in the intergenic regions
database       summary

 TESS
Transcription element search system
database       summary

 TRANSCompel^® Kel-Margoulis, O.¹, Kel, A.¹, Reuter, I.¹, Deineko, I.², Wingender, E.¹
Transcriptional regulation, composite regulatory elements
database       summary

 TRANSPATH^® Krull, M.¹, Pistor, S.¹, Voss, N.¹, Kel, A.¹, Reuter, I.¹, Potapov, A.^1,2, Choi, C.¹, Kel-Margoulis, O.¹, Wingender, E.^1,2
Signal transduction pathways, vizualization and expression data analysis
database       summary

 Transterm Jacobs, G.², Rackham, O.¹, Stockwell, P. A.¹, Brown, C. M.¹
Codon usage, start and stop signals
database       summary

 TRED - Transcriptional Regulatory Element Database
Transcriptional regulatory element database
database       summary

 TRRD Kolchanov N.A.^1,2, Ananko E.A.^1,2, Podkolodnaya O.A.^1,2, Ignatieva E.V.^1,2, Stepanenko I.L.^1,2, Khlebodarova T.M.^1,2, Merkulova T.I.^1,2, Podkolodny N.L.^1,2, Grigorovich D.A.^1,2, Poplavsky A.S.^1,2, Romashchenko A.G.^1,2
Transcription regulatory regions of eukaryotic genes
database       summary

 TrSDB
Transcription factor database
database       summary

PLACE Higo, K.
Plant cis-acting regulatory elements
database       summary

PlantCARE Rombauts, S.¹, Bonnet, E.¹, Thijs, G.³, Marchal, K.³, Moreau, Y.³, Van de Peer, Y.¹, Rouze, P.²
Plant cis-acting regulatory elements
database       summary