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Research Tools
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CpG Island Searcher
(PA Jones Lab)
The CpG island searcher screens for CpG islands which meet the criteria selected below in submitted DNA sequences.
http://www.uscnorris.com/cpgislands/cpg.cgi
Added: Thu Oct 30 2003, Hits: 1563, Reviews: 0 Write review Cached -
CpG Plot
(EBI)
Detection of regions of genomic sequences that are rich in the CpG pattern is important because such regions are resistant to methylation and tend to be associated with genes which are frequently switched on. Regions rich in the CpG pattern are known as CpG islands. The function of the program cpgplot is to plot CpG rich areas, and cpgreport to report all CpG rich regions.
http://www.ebi.ac.uk/emboss/cpgplot/
Added: Thu Oct 30 2003, Hits: 2287, Reviews: 0 Write review Cached -
Dragon Promoter Finder
(Knowledge Extraction Lab, A*STAR)
It searches for and locates promoters in anonymous genomic size DNA sequences. The program 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,
http://research.i2r.a-star.edu.sg/promoter/promote...
Added: Sat Aug 05 2006, Hits: 942, Reviews: 0 Write review -
FirstEF - first-exon and promoter prediction program for human DNA
(Ramana Davuluri et al. CSHL)
FirstEF* (First Exon Finder) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential first donor sites and CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first donor site (GT) and an upstream promoter region, FirstEF decides whether or not the intermediate region can be a potential first exon, based on a set of quadratic discriminant functions.
http://rulai.cshl.edu/tools/FirstEF/
Added: Sat Aug 05 2006, Hits: 564, Reviews: 0 Write review Cached -
McPromoter MM - The Markov Chain Promoter Prediction Server
(Uwe Ohler, University of Erlangen-Nuremberg)
McPromoter is a program aiming at the exact localization of eukaryotic RNA polymerase II transcription start sites. Sensitivity and specificity are now at about 40-50% for both vertebrate and Drosophila at the transcript level
http://genes.mit.edu/McPromoter.html
Added: Sat Aug 05 2006, Hits: 508, Reviews: 0 Write review Cached -
Neural Network Promoter Prediction (NNPP)
(Berkeley Drosophila Genome Project )
One of the best promoter prediction program. NNPP is a method that finds eukaryotic and prokaryotic promoters in a DNA sequence. The basis of the NNPP program is a time-delay neural network
http://www.fruitfly.org/seq_tools/promoter.html
Added: Sat Aug 05 2006, Hits: 554, Reviews: 0 Write review Cached -
Promoter 2.0 Prediction Server
(Steen Knudsen )
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 regions. It builds on principles that are common to neural networks and genetic algorithms.
http://www.cbs.dtu.dk/services/Promoter/
Added: Thu Oct 30 2003, Hits: 1691, Reviews: 0 Write review Cached -
WWW Promoter Scan
(BioInformatics & Molecular Analysis Section, NIH )
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
http://bimas.dcrt.nih.gov/molbio/proscan/
Added: Fri Oct 31 2003, Hits: 1107, Reviews: 0 Write review Cached