GENE FINDING     


 Gene Mark

               A family of gene prediction programs . Includes :
                          Prokaryotic Genomic Sequence Analysis
                         Eukaryotic Genomic Sequence Analysis
                         EST and cDNA Analysis
                         Small Genome (Virus, Phage) DNA Analysis
                  Gene finder based on generalized Hidden Markov Models
                  Finds splice sites and protein coding exons, construct gene model and recognize the promotor and poly-A region


                 Identification of complete gene structures in genomic DNA .Predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.

GenView 2

                  Protein-Coding Gene Prediction

Grail (will put the link soon)


                 Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA

  NetPlantGene V2.0

               Neural network predictions of splice site prediction in Arabidopsis thaliana DNA

 NetGene 2

               Neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

ORF Finder

              The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.

ORF Gene - Gene Structure Prediction using Homologous Proteins.

WWW Promoter Scan

                   Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.

Splice Predictor

                    A method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models

Easy Gene

                  Produces a list of predicted genes given a sequence of prokaryotic DNA. Each prediction is attributed with a significance score (R-value) indicating how likely it is to be just a non-coding open reading frame rather than a real gene.

Gene Publisher

                 This server accepts gene tables or Affymetrix CEL files as input, performs numerical and statistical analysis, links the results to various databases, and returns a report of the results. (Previously known as GeneMachine).


                Software system for gene prediction in complete bacterial genomes and large genomic fragments.


               DNA Structural Analysis of Sequenced Microbial Genomes


               Prediction of vertebrate and C. elegans genes

Net Start

                The NetStart server produces neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences.

Promotor 2

                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.


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