Bruce Ritchings wrote:
>> Hello Netters,
> Can someone point me to a source for codon frequency tables for:
> 1) human
> 2) mouse
> 3) Drosophila
>> Optimally, it would be great to have them in a computer format which would
> plug right into the GCG software, but I'll be grateful for anything I can get!
>> Thanks in advance, Bruce Ritchings
>>britchings at ucsd.edu
Hi!
Look for these in: ftp.ebi.ac.uk/pub/databases/codonusage/
I append the readme file with the list of codon frequency tables
contained in this directory
HELP CODONUSAGE
The directory /pub/databases/codonusage contains tables of codon
frequencies,
calculated for different organisms. At the moment all tables are in the
format
required by the GCG software package. The tables are kindly provided by
Mike
Cherry from Massachusetts General Hospital
(cherry at frodo.mgh.harvard.edu). For
similar data see /pub/databases/CUTG.
The following files are available in the /pub/databases/codonusage
directory:
O asn.cod - Aspergillus nidulans
O ath.cod - Arabidopsis thaliana
O bly.cod - Hordeum vulgare (Barley)
O bmo.cod - Bombyx mori (Silk Moth)
O bov.cod - Bos taurus (Cow)
O bsu.cod - Bacillus subtilis
O cel.cod - Caenorhabditis elegans
O chi.cod - Chironomus sp.
O chk.cod - Gallus sp. (Chicken)
O ddi.cod - Dictyostelium discoideum
O dro.cod - Drosophila melanogaster
O eco.cod - Escherichia coli
O ham.cod - Cricetulus sp. & Mesocricetus
sp.
(Hamster)
O hum.cod - Homo sapiens
O kpn.cod - Klebsiella pneumoniae
O mac.cod - Macaca sp
O mus.cod - Mus sp. (Mouse)
O mze.cod - Zea mays (Maize)
O mzecp.cod - Zea mays chloroplast (Maize)
O neu.cod - Neurospora crassa
O ngo.cod - Neisseria gonorrheae
O pea.cod - Pisum sativum (Pea)
O pet.cod - Petunia sp.
O pfa.cod - Plasmodium falciparum
O phv.cod - Phaseolus vulgaris (Lima bean)
O pot.cod - Solanum tuberosum (Pototoe)
O pse.cod - Pseudomonas sp.
O rab.cod - Oryctolagus sp. (Rabbit)
O rat.cod - Rattus sp. (Rat)
O rhm.cod - Rhizobium meliloti
O ric.cod - Oryza sativa (Rice)
O shp.cod - Ovis sp. (Sheep)
O slm.cod - Physarum polycephalum
O soy.cod - Glycine max (Soybean)
O sta.cod - Staphylococcus aureus
O sty.cod - Salmonella thphimurium
O sus.cod - Strongylocentrotus purpuratus
O tob.cod - Nicotiana tabacum (Tobacco)
O tobcp.cod - Nicotiana tabacum chloroplast
(Tobacco)
O tom.cod - Lycopersicon esculentum (Tomato)
O trb.cod - Trypanosoma brucei
O wht.cod - Triticum aestivum (Wheat)
O xel.cod - Xenopus laevis
O ysc.cod - Saccharomyces cerevisiae
O yscmt.cod - Saccharomyces cerevisiae
mitochondrion
O ysp.cod - Schizosaccharomyces pombe
