New models for GeneMark (gene prediction program)

[William S. Hayes]

Website for GeneMark:  http://amber.biology.gatech.edu/~genemark

New organisms

Matrix Name              Species
-----------              -------------------------------------
burgdorferi              Borrelia burgdorferi       
radiodurans              Deinococcus radiodurans                  
thermo                   Methanobacterium thermoautotrophicum             
mpneu                    Mycoplasma pneumoniae (TGA = Trp)    
furiosis                 Pyrococcus furiosus
prowazekii               Rickettsia prowazekii                 
pyogenes                 Streptococcus pyogenes
pallidum                 Treponema pallidum 



Full listing of available organisms for gene prediction:


Matrix Name              Species
-----------              -------------------------------------
arab                     Arabidopsis thaliana                    
subt                     Bacillus subtilis                       
phi80                    Bacteriophage PHI80                     
t4                       Bacteriophage T4                 
burgdorferi              Borrelia burgdorferi       
bjap                     Bradyrhizobium japonicum                
celegans                 Caenorhabditis elegans
radiodurans              Deinococcus radiodurans                  
fruitfly                 Drosophila melanogaster                 
ebv                      Epstein-Barr virus                      
ehv2                     Equine herpesvirus II                   
ecoli                    Escherichia coli "native" genes [DEFAULT]
ecohiexp                 Escherichia coli highly expressed genes 
ecophage                 Escherichia coli horizontally transferred genes
chicken                  Gallus gallus                           
giardia                  Giardia lamblia                         
flu                      Haemophilus influenzae                  
pylori                   Helicobacter pylori                     
saimiri                  Herpesvirus saimiri                     
human                    Homo sapiens                            
hcmv                     Human Cytomegalovirus                   
kpneu                    Klebsiella pneumonia                    
lacto                    Lactococcus species                       
urchin                   Lytechinus pictus                       
mouse                    Mus musculus         
thermo                   Methanobacterium thermoautotrophicum             
jann                     Methanococcus jannaschii      
leprae                   Mycobacterium leprae                    
tuberc                   Mycobacterium tuberculosis              
capri                    Mycoplasma capricolum (TGA = Trp)       
genit                    Mycoplasma genitalium (TGA = Trp)   
mpneu                    Mycoplasma pneumoniae (TGA = Trp)    
gono                     Neisseria gonorrhoeae
rice                     Oryzae sativa                           
furiosis                 Pyrococcus furiosus
rat                      Rattus norvegicus  
rhizolegum		 Rhizobium leguminosarum
rhizomel		 Rhizobium meliloti                    
rhodo                    Rhodobacter capsulatus 
prowazekii               Rickettsia prowazekii                 
yeast                    Saccharomyces cerevisiae                
salm                     Salmonella typhimurium                  
spombe                   Schizosaccharomyces pombe               
saureus                  Staphylococcus aureus                   
pyogenes                 Streptococcus pyogenes
solf                     Sulfolobus solfataricus   
syn                      Synechocystis              
theil                    Theileria parva 
pallidum                 Treponema pallidum 
volvox			 Volvox carteri                       
frog                     Xenopus laevis