In Silico Promoter prediction:

Promoter can be predicted using various software's. Sometimes, these programs may not produce reliable results.

Note: The list of program given here is partial. There are lot of other programs available.

For a detailed description of how the promoter prediction programs work, read a review by Dan S. Prestridge in the chapter "Computer Software for Eukaryotic Promoter Analysis" from Methods in Molecular Biology, Vol. 130, Transcription factor protocols Edited by: M. J. Tymms (1999), Humana Press Inc., Totowa, NJ.

Promoter-Inspector: Prediction is based on context specific features which were extracted from training sequences (all mammalian sequences) by a heuristic free approach. The novel idea of the PromoterInspector approach is the way of feature definition: Features are defined by equivalence classes of IUPAC groups which allow a fuzzy description of the promoter context. A prediction is based on the analysis of feature frequencies.

FirstEF: 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.

Neural Network Promoter Prediction: The basis of the NNPP program is a time-delay neural network. The time-delay network consists mainly of two feature layers, one for recognizing the TATA-box and one for recognizing the "Initiator", which is the region spanning the transcription start site. Both feature layers are combined into one output unit, which gives output scores between 0 and 1.

TSSG/W: Algorithm predicts potential transcription start positions by linear discriminant function combining characteristics describing functional motifs and oligonucleotide composition of these sites.

Promoter Scan: 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 

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