Promoter finders
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Promoter Finder BDGP: Neural Network Promoter Prediction.. Searches Home. About BDGP. Contact Information, News, Citing BDGP Searches. Fly BLAST. GadFly. Genome Annotations FlyBase All Searches. FlyBase, BDGP, EDGP Analysis Tools. Projects. Genomic ...
Promoter scan
WWW Promoter Scan Function. : Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences. The analysis. is done using the PROSCAN Version 1.7 suite of programs developed by Dr. Dan Prestridge. ...
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Promoter 2.0 Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in.
Promoter Finder Searches for and locates promoters in anonymous vertebrate genomic size DNA sequences. Attempts to recognize the exact location of the transcription start site (TSS), i.e. the 1 position relative to the TSS. The analysis is strand specific. The algorithm is designed and tuned for a high specificity search, meaning that, in general, it will produce a small number of false positive predictions.
TFSearch Searching DNA for transcription Factor Binding Sites (searches TransFAC).
PromoSer
Large-scale mammalian promoter and transcription start site identification service. web service that facilitates extraction of user specified regions around the transcription start site of all annotated human, mouse or rat genes. The transcription start sites have been identified computationally by considering alignments of a large number of partial and full-length mRNA sequences to genomic DNA, with provision for alternative promoters.
MatInspector v2.2 Search for potential binding sites with MatInspector V2.2 now based on TRANSFAC 4.0.
Gene Start Finder Predicts 5-prime region in mammalian DNA. Dragon GSF is a system that attempts to predict the 5-prime region of the transcriptional unit of a gene in anonymous mammalian DNA. The system uses a combination of different sensors to predict a region that is expected to overlap or to be in close proximity of the first exon of the transcriptional unit.
GC Promoter Finder Dragon GC Promoter Finder is a system that attempts to predict promoters in GC rich regions.
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Place A Database of Plant Cis-acting Regulatory DNA Elements.
RSAT
Software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, and random sequence generation
Regulatory Sequence Analysis Tools for prediction of regulatory sites in non-coding DNA sequences. Tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds more than fully sequenced genomes and these data are regularly updated from GenBank.
rMotif
Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Interface for automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles. The server provides a wide spectrum of analysis tools that allow de novo discovery of regulatory motifs, along with refinement and in-depth investigation of fully or partially characterized motifs. The presented discovery and analysis tools are fundamentally different from existing tools in their basic rational, statistical background and specificity and sensitivity towards true regulatory elements.
Improbizer Improbizer. Improbizer searches for motifs in DNA or RNA sequences that occur with improbable frequency (to be just chance) using a variation of the expectation maximization (EM) algorithm. Enter in sequences in the large box below - ...
:: RHUL Pattern Recognition Techniques Server ::
Plant promoter and prokaryotic promoter prediction tools and demos, including an excellent Escherichia coli promoter map.
PlantCARE, a databse of plant promoters and their cis-acting
Databse of plant promoters and their cis-acting regulatory elements. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Includes 435 different plant ...
Composite Module Analyst (CMA)
Defining promoter models based on the composition of transcription factor binding sites and their pairs. Composite modules (CM). Combinations of binding sites common for promoters of functionally related genes and responsible for the major ...
