The files in this directory contain optimal growth temperatures and
genomic G+C content for bacterial species. See Galtier and Lobry (1997)
Columns are separated by tabulation characters ('\t'), missing values
are indicated by a star ('*'), there are no column headers.
There are seven files. The file "species" contains optimal growth
temperature and genomic G+C content by species. The file "genus"
contains optimal growth temperature and genomic G+C content by genus.
The file "details" contains raw data with full details. The files
"16S.txt", "23S.txt", "5S.txt" and "tRNA.txt" contain the data
corresponding to Figure 1 in Galtier & Lobry (1997).
The 772 lines are bacterial species. There are 4 columns:
4) Optimal growth temperature in C degree
The 224 lines are bacterial genus. There are 4 columns:
3) The average optimal growth temperature in C degree.
4) The number of species in the genus that were available to
compute the average Topt and G+C content.
The 772 lines are bacterial species. There are 8 columns:
3) Lower bound for G+C content (Tm determination)
4) Upper bound for G+C content (Tm determination)
5) Lower bound for G+C content (Bd determination)
6) Upper bound for G+C content (Bd determination)
The 165 lines are bacterial genus. There are 3 colums:
2) Optimal growth temperature in C degree
The 51 lines are bacterial genus. There are 3 colums:
The 38 lines are bacterial genus. There are 3 colums:
The 71 lines are bacterial genus. There are 3 colums:
Galtier, N. & Lobry, J.R. (1997). Relationships between genomic G+C
content, RNA secondary structures, and optimal growth temperature
in prokaryotes. Journal of Molecular Evolution 44:632-636.
Note: this section was deleted on import because of encoding issues.
19-MAR-1997: Files put on anonymous ftp server at the URL:
02-NOV-2000: Data corresponding to Fig 1 and forward bibliography added.

# This R script was used to import data from that were on
# ftp://biom3.univ- lyon1.fr/pub/dataset/JME97 and then
# According to the README file the last update was
gcT <- vector(mode = "list", length = 9)
names(gcT) <- c("species", "genus", "details", "gc16S", "gctRNA", "gc23S", "gc5S", "README", "importgcT")
# Import data and check againts README for dimensions and number of NA
species <- read.table(paste(path, "species", sep = "/"), sep = "\t", na.string = "*")
colnames(species) <- c("Genus", "species", "GC", "Topt")
genus <- read.table(paste(path, "genus", sep = "/"), sep = "\t", na.string = "*")
colnames(genus) <- c("Genus", "GC", "Topt", "nSpe")
details <- read.table(paste(path, "details", sep = "/"), sep = "\t", na.string = "*")
colnames(details) <- c("Genus", "species", "GCminTm", "GCmaxTm", "GCminBd", "GCmaxBd", "Toptmin", "Toptmax")
gc16S <- read.table(paste(path, "16S.txt", sep = "/"), sep = "\t", na.string = "*")
colnames(gc16S) <- c("Genus", "Topt", "GC")
gctRNA <- read.table(paste(path, "tRNA.txt", sep = "/"), sep = "\t", na.string = "*")
colnames(gctRNA) <- c("Genus", "Topt", "GC")
gc23S <- read.table(paste(path, "23S.txt", sep = "/"), sep = "\t", na.string = "*")
colnames(gc23S) <- c("Genus", "Topt", "GC")
gc5S <- read.table(paste(path, "5S.txt", sep = "/"), sep = "\t", na.string = "*")
colnames(gc5S) <- c("Genus", "Topt", "GC")
gcT[["README"]] <- readLines(paste(path, "README", sep = "/"))
#Delete forward biblio with encoding problems:
gcT[["README"]][84] <- "  Note: this section was deleted on import because of encoding issues."