Gene Prediction Methods
From DrugPedia: A Wikipedia for Drug discovery
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
[edit] 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 |
