E.coli codon usage

Don Gilbert gilbertd at chipmunk.bio.indiana.edu
Thu Feb 18 18:11:30 EST 1993


In article <2A50C086 at coursmtp.nrc.ca> pbonham at pbi.lan.nrc.ca writes:
>Does anyone out there have a computed version of E.coli preferred codon usage
>or know where I can get hold of one?
>Please reply via the network
>

via Internet Gopher or anonymous ftp to ftp.bio.indiana.edu,
look in folder  /molbio/codon for eco.cod
::::: eco.cod :::::

Escherichia coli

681 genes found in GenBank 63.

 Produced by J. Michael Cherry (cherry at frodo.mgh.harvard.edu) with the
 GCG program CodonFrequency.
....

and data. There are even a few plant codon preference files here:

File Name	Organism/Organelle
==========	======================================================
ALGAE.COD	Chlorella sp., Chlamydomonas sp., & Euglena sp. (Green Algae)
anopheles.codon Anopheles gambiae (mosquito)
ASN.COD		Aspergillus nidulans
ATH.COD		Arabidopsis thaliana
BLY.COD		Hordeum vulgare (Barley)
BMO.COD		Bombyx mori (Silk Moth)
BOV.COD		Bos taurus (Cow)
BSU.COD		Bacillus subtilis
CEL.COD		Caenorhabditis elegans
CHI.COD		Chironomus sp.
CHK.COD		Gallus sp. (Chicken)
DDI.COD		Dictyostelium discoideum
DRO.COD		Drosophila melanogaster
ECO.COD		Escherichia coli
HAM.COD		Cricetulus sp. & Mesocricetus sp. (Hamster)
HUM.COD		Homo sapiens
KPN.COD		Klebsiella pneumoniae
MAC.COD		Macaca sp
MUS.COD		Mus sp. (Mouse)
MZE.COD		Zea mays (Maize)
MZECP.COD	Zea mays chloroplast (Maize)
NEU.COD		Neurospora crassa
NGO.COD		Neisseria gonorrheae
PEA.COD		Pisum sativum (Pea)
PET.COD		Petunia sp.
PFA.COD		Plasmodium falciparum
PHV.COD		Phaseolus vulgaris (Lima bean)
POT.COD		Solanum tuberosum (Potatoe)
PSE.COD		Pseudomonas sp.
RAB.COD		Oryctolagus sp. (Rabbit)
RAT.COD		Rattus sp. (Rat)
RHM.COD		Rhizobium meliloti
RIC.COD		Oryza sativa (Rice)
SHP.COD		Ovis sp. (Sheep)
SLM.COD		Physarum polycephalum
SOY.COD		Glycine max (Soybean)
STA.COD		Staphylococcus aureus
STY.COD		Salmonella thphimurium
SUS.COD		Strongylocentrotus purpuratus
TOB.COD		Nicotiana tabacum (Tobacco)
TOBCP.COD	Nicotiana tabacum chloroplast (Tobacco)
TOM.COD		Lycopersicon esculentum (Tomato)
TRB.COD		Trypanosoma brucei
WHT.COD		Triticum aestivum (Wheat)
XEL.COD		Xenopus laevis
YSC.COD		Saccharomyces cerevisiae
YSCMT.COD	Saccharomyces cerevisiae mitochondrion
YSP.COD		Schizosaccharomyces pombe
-- 
Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405



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