Gene Prediction Methods
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Revision as of 07:19, 5 September 2008
Gene prediction by computational methods for finding the location of protein coding regions is one of the essential issues in bioinformatics.
Two classes of methods are generally adopted:
- similarity based searches
- ab initio prediction
List of Gene Prediction Methods
| NAME | Description | Link |
|---|---|---|
| GENEID | program to predict genes, exons, splice sites and other signals along a DNA sequence | Server |
| BGF | hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program | Server |
| GENEPARSER | Parse a DNA sequence into introns and exons | Server |
| GENEMARK | family of gene prediction programs | Server |
| WEBGENEMARK.HMM | gene prediction program for prokaryotes and eukaryotes | Server |
| AUGUSTUS | predicts genes in eukaryotic genomic sequences | Server |
| ATGpr | identifying translational initiation sites in cDNA sequences | Server |
| GENIUS | linking ORFs in complete genomes to protein 3D structures | Server |
| NIX | web tool for combining results from different programs (GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN) | Server |
| FRAMED | find genes and frameshift in G+C rich procaryotic sequences | Server |
| EUGENE | gene finding for Arabidopsis thaliana | Server |
| GLIMMER | finding genes in microbial DNA | Server |
| VEIL | hidden markov model for finding genes in vertebrate DNA | Server |
| MORGAN | a decision tree system for finding genes in vertebrate DNA | Server |
| SPLICEPREDICTOR | a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models | Server |
| GENESCAN | finding genes using Fourier transform | Server |
| Dragon Promoter Finder | software for recognition of vertebrate RNA Polymerase II promoters | Software |
| NNPP | promoter prediction by neural network | Server |
| NNSPLICE | splice site prediction by neural network | Server |
| Regulatory Sequence Analysis Tools | provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences. | Server |
| GENOMESCAN | predicts locations and exon-intron structures of genes in genomic sequences from a variety of organisms. | Server |
| DIOGENES | a system for fast detection of coding regions in short genomic sequences | Server |
| ORF FINDER | a graphical analysis tool which finds all open reading frames | Server |
| GrailEXP | predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence | Server |
| CDS | search coding regions | source |
| HMMGENE | prediction of vertebrate and c. elegans genes | Server |
| NETGENE2 | intron splice site prediction in human c. elegans, a. thaliana | Server |
| NETPLANTGENE | intron splice site prediction in a. thaliana DNA | Server |
| NETSTART | translation start in vertebrate and a. thaliana DNA | Server |
| PROMOTER | predicts transcription start sites of vertebrate PolII promoters in DNA sequences | Server |
