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codon_usage_metadata.R
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# codon usage tables metadata file
# note that there is a list of everything at the end of this file
# uniform for purposes of testing (all values are 1)
uniform_cu <- list(
name="Uniform",
binomial="Uniformo uniformis",
file="codon_usage/uniform.txt",
format="CUTG GCC",
url=NA,
access_date=NA)
# end of uniform_cu
# virus: lambda, hiv
lambda <- list(
name="Lambda",
binomial="Enterobacteria phage lambda",
file="codon_usage/lambda.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=10710&aa=1&style=GCG",
access_date="30 May, 2014" )
# end of lambda
hiv1 <- list(
name="HIV1",
binomial="Human immunodeficiency virus 1",
file="codon_usage/hiv1.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=11676&aa=1&style=GCG",
access_date="30 May, 2014" )
# end of hiv1
# bacteria: e coli, b subtilis
e_coli <- list(
name="E. coli",
binomial="Escherichia coli",
file="codon_usage/e_coli.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=37762&aa=1&style=GCG",
access_date="30 May, 2014" )
# end of coli
b_subtilis <- list(
name="B. subtilis",
binomial="Bacillus subtilis",
file="codon_usage/b_subtilis.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=1423&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of b_subtilis
# archaea: s. solfataricus, h. volcanii
s_solfataricus <- list(
name="S. solfataricus",
binomial="Sulfolobus solfataricus P2",
file="codon_usage/s_solfataricus.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=273057&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of s_solfataricus
h_volcanii <- list(
name="H. volcanii",
binomial="Haloferax volcanii",
file="codon_usage/h_volcanii.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=2246&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of h_volcanii
# protist: tetrahymena, chlamy
t_thermophila <- list(
name="T. thermophila",
binomial="Tetrahymena thermophila",
file="codon_usage/t_thermophila.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=5911&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of t_thermophila
c_reinhardtii <- list(
name="C. reinhardtii",
binomial="Chlamydomonas reinhardtii",
file="codon_usage/c_reinhardtii.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3055&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of c_reinhardtii
# plant: a. thaliana, rice
a_thaliana <- list(
name="A. thaliana",
binomial="Arabidopsis thaliana",
file="codon_usage/a_thaliana.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3702&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of a_thaliana
rice <- list(
name="O. sativa",
binomial="Oryza sativa",
file="codon_usage/rice.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=311553&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of o_sativa
# fungi: yeast, coprinopsis cinerea
yeast <- list(
name="S. cerevisiae",
binomial="Saccharomyces cerevisiae",
file="codon_usage/yeast.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4932&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of yeast
c_cinerea <- list(
name="C. cinerea",
binomial="Coprinopsis cinerea",
file="codon_usage/c_cinerea.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=5346&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of cinerea
# animal: chicken, fly, human
chicken <- list(
name="G. gallus",
binomial="Gallus gallus",
file="codon_usage/chicken.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9031&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of chicken
fruitfly <- list(
name="D. melanogaster",
binomial="Drosophila melanogaster",
file="codon_usage/fruitfly.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7227&aa=1&style=GCG",
access_date="2 June, 2014" )
# end of fruitfly
human <- list(
name="Human",
binomial="Homo sapiens",
file="codon_usage/human.txt",
format="CUTG GCC",
url="http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606&aa=1&style=GCG",
access_date="21 May, 2014" )
# end of human
# all
all_cus <- list(uniform_cu, lambda, hiv1, e_coli, b_subtilis, s_solfataricus, h_volcanii, t_thermophila, c_reinhardtii, a_thaliana, rice, yeast, c_cinerea, chicken, fruitfly, human )