List of gene prediction software

In today's world, List of gene prediction software is a topic of great relevance and interest to a wide spectrum of society. Whether it's a current topic, a prominent figure, a historical event, or any other area of ​​importance, List of gene prediction software has captured the attention of people of all ages and backgrounds. This attention is due, in part, to the relevance that List of gene prediction software has in people's daily lives, as well as its impact in different areas, such as politics, culture, technology or the economy. This article seeks to further explore the meaning and importance of List of gene prediction software, as well as provide a detailed analysis of its impact on today's society.

This is a list of software tools and web portals used for gene prediction.

Name Description Species References
FINDER Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences Eukaryotes
FragGeneScan Predicting genes in complete genomes and sequencing Reads Prokaryotes, Metagenomes
ATGpr Identifies translational initiation sites in cDNA sequences Human
Prodigal Its name stands for Prokaryotic Dynamic Programming Genefinding Algorithm. It is based on log-likelihood functions and does not use Hidden or Interpolated Markov Models. Prokaryotes, Metagenomes (metaProdigal)
AUGUSTUS Eukaryote gene predictor Eukaryotes
BGF Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program
DIOGENES Fast detection of coding regions in short genome sequences
Dragon Promoter Finder Program to recognize vertebrate RNA polymerase II promoters Vertebrates
EasyGene The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes
EuGene Integrative gene finding Prokaryotes, Eukaryotes
FGENESH HMM-based gene structure prediction: multiple genes, both chains Eukaryotes
FrameD Find genes and frameshift in G+C rich prokaryote sequences Prokaryotes, Eukaryotes
GeMoMa Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data
GENIUS II Links ORFs in complete genomes to protein 3D structures Prokaryotes, Eukaryotes
geneid Program to predict genes, exons, splice sites, and other signals along DNA sequences Eukaryotes
GeneParser Parse DNA sequences into introns and exons Eukaryotes
GeneMark Family of self-training gene prediction programs Prokaryotes, Eukaryotes,

Metagenomes

GeneTack Predicts genes with frameshifts in prokaryote genomes Prokaryotes
GenomeScan Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms, GENSCAN server is the GenomeScan's predecessor Vertebrate, Arabidopsis, Maize
GENSCAN Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms Vertebrate, Arabidopsis, Maize
GLIMMER Finds genes in microbial DNA Prokaryotes
GLIMMERHMM Eukaryotic gene-finding system Eukaryotes
GrailEXP Predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repeat elements in DNA sequence Human, Mus musculus, Arabidopsis thaliana, Drosophila melanogaster
mGene Support-vector machine (SVM) based system to find genes Eukaryotes
mGene.ngs SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays Eukaryotes
MORGAN Decision tree system to find genes in vertebrate DNA Eukaryotes
BioNIX Web tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN Prokaryotes, Eukaryotes
NNPP Neural network promoter prediction Prokaryotes, Eukaryotes
NNSPLICE Neural network splice site prediction Drosophila, Human
ORFfinder Graphical analysis tool to find all open reading frames Prokaryotes, Eukaryotes
Regulatory Sequence Analysis Tools Series of modular computer programs to detect regulatory signals in non-coding sequences Fungi, Prokaryotes, Metazoa, Protist, Plants
PHANOTATE A tool to annotate phage genomes. Phages
SplicePredictor Method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models Eukaryotes
VEIL Hidden Markov model to find genes in vertebrate DNA Server Eukaryotes

See also

References

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