Regulatory Site Finding
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[GSF] Predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. These consensus descriptions produced by the program ConsInd consist of the length of the binding site and the individual conservation of each nucleotide position within the site.
[GSF] This program is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences.
Eukaryotic Promoter Database
[ISREC] An annotated non-redundant collection of eukaryotic POL II promoters, for which the
transcription start site has been determined experimentally.
[BIODV-GSF] A search tool for potential transcription factor binding sites.
ModelGenerator & ModelInspector
[GSF] Methods for generation and recognition of models for regulatory regions in DNA sequences.
[CBS] A World Wide Web server producing neural network predictions of splice sites in human, C. elegans, and A. thaliana DNA.
[CBS] A service producing neural network predictions of splice sites in Arabidosis thaliana DNA.
[CBS] Produces network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences.
Neural Network Promoter Prediction
[Berkeley Drosophila Genome Project] Allows the user to enter DNA sequences to find possible transcription promoters.
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PROMOTER SCAN II
[National Institute of Health] PROMOTER SCAN II is a program developed to recognize and predict pol II promoters in genomic DNA sequences. Presently it is limited to mammalian promoter sequences, and is set to find approximately 50% of promoter sequences never before seen by the program, with an expected false positive rate of about 1 in 15,000 single-stranded bases. The program recognizes TATA-containing as well as TATA-less promoters.
Regulatory Sequence Analysis Tools
[Laboratorio de Biologia Computacional] A series of modular computer programs specifically designed for
the detection of regulatory signals in non-coding sequences.
SSPN: Splice Site Prediction by Neural Network
[Berkeley Drosophila Genome Project] Takes a DNA sequence and finds the possible 5′ and 3′ splice sites.
[University of Pennsylvania] [Annotation pending]
[Parallel Application TRC Laboratory, Computational Biology Research Center] Searches for transcription factor binding sites in DNA sequences.
TraFaC Homology Server
[UC/CHMC] Trafac identifies conserved cis-elements/transcription factor binding sites by adopting a comparative genomic analysis of orthologous
DNA sequences. It can also be used to find whether coordinately regulated genes share common cis-elements.
[GBF] A database program that compiles data about gene regulatory DNA sequences; from this data programs have been developed to identify putative promoter or enhancer structures.
WWW Promoter Scan
[BioInformatics & Molecular Analysis Section (BIMAS)] Predicts promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.