Top : Research Tools : Online Tools : Sequence Analysis : Promoter and CpG island Prediction
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Protocols
  • 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: 8757, 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: 6329, Reviews: 0  Write review   Cached
  • Tool/Software 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.org/tools/FirstEF/
    Added: Sat Jan 31 2009, Hits: 2473, Reviews: 0  Write review   Cached
  • Tool/Software 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 Jan 31 2009, Hits: 2362, 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: 4079, 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: 2881, Reviews: 0  Write review   Cached

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