Gene Identification

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Gene Identification - Quick Links Edit

GenScan Softberry
GeneID GenScan
GeneBuilder GenView
WebGene Alternative Splicing Database
Glimmer GlimmerM
GeneMark HMM Genie
HomoloGene X-Grail
Wise2 GeneFizz
AGenDA FrameD
Manatee GeneComber
RiceHMM Unveil
E-Matrix DMGF
GeneZilla Augustus: job submission
GeneMark (EBI server) ZCURVE
Gismo MetaGene

Gene Identification - Web Resources Edit

GenScan A general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants. Identification of complete gene structures in genomic DNA. Identifies complete exon/intron structures of genes in genomic DNA. GENSCAN has been shown to have higher accuracy than existing methods when tested on standardized sets of human and vertebrate genes, with 75 to 80% of exons identified exactly. The program is also capable of indicating fairly accurately the reliability of each predicted exon. Consistently high levels of accuracy are observed for sequences of differing C G content and for distinct groups of vertebrates. Changes have been made to improve the accuracy of the program for plant sequences. For maize, these changes actually resulted in slightly lower nucleotide-level accuracy relative to the vertebrate parameter set, but this is more than compensated by the greatly improved exon-level accuracy numbers. For Arabidopsis, the improvement is more even, with higher accuracy seen in almost every category. <pubmed argument="GenScan">9149143</pubmed>

Softberry offers a number of Gene Finding tools for Eukaryota and Bacteria.

DPL Forum: Too few categories!

GeneID Predicts genes, exons, splice sites and other signals along a DNA sequence. Gene prediction based on human, fruit fly, puffer fish, slime mold or wheat. May provide enhancements over GenScan.

GenScan Gene modelling, Europe.

GeneBuilder GeneBuilder Gene Structure Prediction System Organism: Homo sapiens Mus musculus Fugu Caenorhabditis elegans Drosophila melanogaster Arabidopsis thaliana Aspergillus niger Mode: Gene Exon Strand: Direct Complement Sequencing error ...

GenView TOOLS FOR PREDICTION AND ANALYSIS OF PROTEIN-CODING GENE STRUCTURE. An integrated computing system for protein-coding gene prediction.. Repeated elements mapping.. CpG islands prediction.. Splicing signals prediction.. Hamming Clustering ...

WebGene Tools for prediction and analysis of protein-coding gene structure.

Alternative Splicing Database This page uses frames but your browser does not support them This page uses frames but your browser does not support them

Glimmer Find genes in microbial DNA esp. bacterial - Gene Locator and Interpolated Markov Modeler. 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.

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GlimmerM Ab initio eukaryotic gene finder derived from Glimmer, but developed specifically for eukaryotes. A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The de

GeneMark A family of gene prediction programs developed by Mark Borodovsky's Bioinformatics Group at the Georgia Institute of Technology, Atlanta, Georgia. Coding probability of single exon, Borodovsky and Lukashin.

HMM Genie Gene Finder Based on Generalized Hidden Markov Models.

HomoloGene HomoloGene is a resource of curated and calculated orthologs for genes as represented by UniGene or by annotation of genomic sequences.

X-Grail Coding probability of single exons, Gene Recognition and Assembly Internet Link.

EUGENE-HOM Generic similarity-based gene finder using multiple homologous sequences. Gene prediction software for eukaryotic organisms based on comparative analysis. EUGENE-HOM is able to take into account multiple homologous sequences from more or less closely related organisms. It integrates the results of TBLASTX analysis, splice site and start codon prediction and a robust coding/non-coding probabilistic model which allows EUGENE-HOM to handle sequences from a variety of organisms. The current target of EUGENE-HOM is plant sequences.<pubmed argument="EUGENE-HOM">12824408</pubmed>

GeneNest GeneNest is a comprehensive visualization of gene indices of the following organisms: human, mouse, Arabidopsis, Drosophila and zebrafish. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artefacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms.<pubmed argument="GeneNest">12199289</pubmed>

Wise2 Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

GeneFizz Web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives. Permits direct comparison between two types of segmentations for DNA sequences (possibly annotated): the coding/non-coding segmentation associated with genomic annotations (simple genes or exons in split genes) and the physics-based structural segmentation between helix and coil domains (as provided by the classical helix-coil model). There appears to be a varying degree of coincidence for different genomes between the two types of segmentations, from almost perfect to non-relevant. Following these two extremes, GeneFizz can be used for two purposes: ab initio physics-based identification of new genes (as recently shown for Plasmodium falciparum) or the exploration of possible evolutionary signals revealed by the discrepancies observed between the two types of information.<pubmed argument="GeneFizz">12824434</pubmed>

AGenDA Alignment-based Gene Detection Algorithm. AGenDA is a gene-prediction tool that is based on cross-species sequence comparison. The software tools CHAOS and DIALIGN are used to align a pair of syntenic genomic sequences, e.g. from human and mouse. AGenDA searches for conserved splice sites and start/stop codons at the boundaries of identified sequence homologies in order to identify potential exons these potential exons are then used to assemble entire gene models.

FrameD Program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. <pubmed argument="FrameD">12824407</pubmed>

Manatee Web-based gene evaluation and genome annotation tool. MANATEE is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments

GeneComber GeneComber is a graphical interface to the output of several ab initio gene prediction algorithms. Implements novel methods for combining predictions from programs Genscan and HMMgene. These methods primarily aim to improve exon level accuracy of gene-finding by identifying more probable exon boundaries and by eliminating false positive exon predictions. This approach results in improved accuracy at both the nucleotide and exon level, especially the latter, where the average improvement on the newly assembled dataset is 7.9% compared to the best result obtained by Genscan and HMMgene. When tested on a long genomic multi-gene sequence, our method that maintains reading frame consistency improved nucleotide level specificity by 21.0% and exon level specificity by 32.5% compared to the best result obtained by either of the two programs individually.<pubmed argument="GeneComber">12176826</pubmed>

RiceHMM Search: !?. About RGP. What's New. Research. Research achievements. Link. RiceHMM Gene Prediction Program for Rice RiceHMM predicts gene domains on rice genome sequence based on probabilistic model using a catalog of rice ESTs. The gene ...

Unveil Ab initio eukaryotic gene finder based on a 283-state Hidden Markov Model (HMM). Unveil is a new gene finder based on a 283-state Hidden Markov Model (HMM) similar to that described in [Henderson,J., Salzberg,S., and Fasman,K.H. (1997) J. Comput. Biol. 4, 127-141].

E-Matrix Rapid identification of proteins based upon fast probabilistic analysis of sequence function using scoring matrices.

DMGF Dictionary driven microbial gene finding.

GeneZilla Eukaryotic gene finder formerly known as TigrScan. GeneZilla is a state-of-the-art program for computational prediction of protein-coding genes in eukaryotic DNA, and is based on the Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN

Augustus: job submission Predicts genes in eukaryotic genomic sequences using hints compounded from EST and protein databases, able to predict 89% of the exons in human chromosome 22 correctly. Trained to predict genes in human, fruit fly, Arabidopsis and many others.

GeneMark (EBI server) Site search ?. .. .. SEQUENCE ANALYSIS. Help Index. General Help. Formats. Gaps. Matrix. References. Genemark Help. GeneMark Submission Form The GeneMark program is accessing the coding potential of DNA sequences by using Markov models of ...

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