AAT - Analysis and Annotation Tool (Michigan Tech University)
Identifies genes by comparing cDNA and protein sequence databases.
ECOPARSE (The Technical University of Denmark)
A mailserver for finding genes in E. coli DNA.
FGENEH (Baylor)
Predicts a single complete gene and the
corresponding amino acid sequence. (FEXH, HEXON, GENEFINDER)
GENEID (IMIM-UPF)
An AI system for examining human and drosophila genomic DNA and prediction of exons and
gene structure.
GENEMARK (Georgia Tech)
A genefinding tool that uses an algorithm
based on non-homogenous Markov chain models.
GENEPARSER (University of Colorado)
A coding region recognition program
that uses potential similarity between query sequence and known amino acid
sequences.
GENSCAN (MIT)
Predicts complete gene structures (exons, introns, promoter and polyA
signals in genomic sequences.
Genie(LBNL)
Gene finder based on generalized hidden Markov models to locate multi-exon
genes.
GENLANG (University of Pennsylvania)
A syntactic pattern recognition system that uses tools of computational
linguistics to find genes.
GLIMMER (John Hopkins University)
Uses interpolated Markov models to find genes in microbial DNA.
GRAIL (ORNL)
Provides analysis and annotation of DNA sequences both interactively and
through the use of automated computation. (Includes GenQuest, Grail v1.3
and Xgrail)
METAGENE (Medical College of Wisconsin)
MetaGene is a powerful tool designed to provide exhaustive analysis of predicted gene
features in sequence. It allows the researcher to submit sequences against different gene
prediction engines simultaneously to obtain a comprehensive report on sequence features.
MZEF (CSHL)
Predicts internal protein coding exons in genomic DNA sequences.
MORGAN(John Hopkins University)
A decision tree program for finding genes invertebrate DNA.
NetGene2(Denmark)
Provides neural network predictions of splicesites, including Arabidopsis.
PROCRUSTES(University of Southern California) By utilizing the spliced
alignment algorithm, this program examines all possible exon assemblies
and finds the multi-exon structure with the best fit to related protein.
PPNN (LBNL)
Offers promoter prediction by neural network.
REPEATMASKER (University of Washington)
Screens DNA sequences against a library of repetitive elements and returns a masked
query sequence ready for database searches and genefinding programs.
SIGNALSCAN (NIH)
Rather than predicting, this program finds homologies of published signal
sequences in the submitted sequence. This program is best used for
learning the identity of unknown proteins bound to characterized binding
sites in DNA sequences.
SORFIND (RabbitHutch)
Identifies and annotates individual coding exons in genomic DNA sequence.
SPLICEPREDICTOR (Stanford)
Identifies potential splice sites in plant pre-mRNA by sequence inspection.
TESS (University of Pennsylvania)
Transcription elementsearch software for locating and displaying transcription
factor binding sites in DNA sequences.
VEIL (John Hopkins University)
Uses a customized hidden Markov model to locate genes in vertebrate DNA.
WEBGENE (Institute of Advanced Biomedical Technologies,Italy)
A web interface for several coding region recognition patterns. (GENVIEW)
Wise2 (Sanger)
Provides simultaneous prediction of gene structure with homology based
alignment. |