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codon usage,

Rodrigo Lopez rls at ebi.ac.uk
Fri May 29 05:00:35 EST 1998


Hi,

Try: ftp://ftp.ebi.ac.uk/pub/databases/codonusage/

Here is the readme file:

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


R:)


"Tyamgondlu "Venky" Venkatesh" wrote in message
<19980527174258.00e249dc.in at S2>...
>Dear All
>I would like to  get codon usage table for high and low expressed
>genes in different organisms. I am particularly interested in
>bacteria and  rat/mouse. I would apprecite if somebody can suggest me
>the source.
>Thanks
>Venky


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`
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