Genomes Fish, Aspergillus, Diatom new gene-finding parameters for FGENESH suit

softberry at softberry.com softberry at softberry.com
Mon Sep 15 10:58:37 EST 2003


Genomes Fish, Aspergillus, Diatom new gene-finding parameters for FGENESH suit

A new parameter set for gene annotation in Fish, Diatom, Aspergillus genomes
is presented for FGENESH program suit. Accuracy of coding region 
identification 
by Fgenesh is about 98% on the nucleotide level. 

New parameters can be used with: 

FGENESH / HMM-based gene structure prediction (multiple genes, both chains) 

BESTORF / Finding potential coding fragment EST/mRNA 

FEX / Finding potential 5'-, internal and 3'-coding exons

FGENESH+ / HMM plus similar protein-based gene prediction 

FGENESH_C / HMM plus similar cDNA-based gene structure prediction (multiple 
genes, both chains) 

FGENESH-2 / HMM gene prediction using two genomic sequences of close organisms 
(as Human and Mouse)


the programs with parameters for major model organisms 
  is available for on line usage at: 

http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind

Totally specific parameters of gene-finding is available for

Human, Mouse, Drosophila, C.elegans, Dicots (Arabidopsis), Nicotiana tabacum, 
Monocots (Corn, Rice, Wheat, Barley), Schizosaccharomyces pombe, Neurospora 
crassa,
Plasmodium falciparum, Anopheles gambiae, Fish, Diatom, Aspergillus  

FGENESH is the fastest and most accurate ab initio gene prediction program 
available based on HMM approach. 


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