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DESCRIPTION","-------------------","","The files in this directory contain optimal growth temperatures and","genomic G+C content for bacterial species. See Galtier and Lobry (1997)","for more details.","","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).","","FILE DESCRIPTION","----------------","","The file \"species\".","The 772 lines are bacterial species. There are 4 columns:","1) Genus names","2) Species names","3) G+C content in percent","4) Optimal growth temperature in C degree","Number of missing values: 0","","The file \"genus\".","The 224 lines are bacterial genus. There are 4 columns:","1) Genus names.","2) The average G+C content in percent.","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.","Number of missing values: 0","","The file \"details\"","The 772 lines are bacterial species. There are 8 columns:","1) Genus names","2) Species names","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)","7) Lower bound for Topt","8) Upper bound for Topt","Number of missing values: 2059","","The file \"16S.txt\"","The 165 lines are bacterial genus. There are 3 colums:","1) Genus name","2) Optimal growth temperature in C degree","3) stems G+C content","","","The file \"tRNA.txt\"","The 51 lines are bacterial genus. There are 3 colums:","1) Genus name","2) Optimal growth temperature in C degree","3) G+C content","","The file \"23S.txt\"","The 38 lines are bacterial genus. There are 3 colums:","1) Genus name","2) Optimal growth temperature in C degree","3) stems G+C content","","The file \"5S.txt\"","The 71 lines are bacterial genus. There are 3 colums:","1) Genus name","2) Optimal growth temperature in C degree","3) G+C content","","","REFERENCES","----------","","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.","","This paper was cited by:","  Note: this section was deleted on import because of encoding issues.","","UPDATES","-------","","19-MAR-1997: Files put on anonymous ftp server at the URL:","             ftp://biom3.univ-lyon1.fr/pub/datasets/JME97/","             ","02-NOV-2000: Data corresponding to Fig 1 and forward bibliography added.","             ","13-MAY-2002: Forward bibliohgraphy updated."],"importgcT":["#","# This R script was used to import data from that were on ","# ftp://biom3.univ- lyon1.fr/pub/dataset/JME97 and then","# relocated to ftp://pbil.univ-lyon1.fr/pub/datasets/JME97","# According to the README file the last update was","# 13-MAY-2002","#","","path <- \"ftp://pbil.univ-lyon1.fr/pub/datasets/JME97\"","","# Make a list to store imported data :","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 = \"*\")","stopifnot(dim(species) == c(772, 4))","stopifnot(sum(is.na(species)) == 0)","colnames(species) <- c(\"Genus\", \"species\", \"GC\", \"Topt\")","gcT[[\"species\"]] <- species","","genus <- read.table(paste(path, \"genus\", sep = \"/\"), sep = \"\\t\", na.string = \"*\")","stopifnot(dim(genus) == c(224, 4))","stopifnot(sum(is.na(genus)) == 0)","colnames(genus) <- c(\"Genus\", \"GC\", \"Topt\", \"nSpe\")","gcT[[\"genus\"]] <- genus","","details <- read.table(paste(path, \"details\", sep = \"/\"), sep = \"\\t\", na.string = \"*\")","stopifnot(dim(details) == c(772, 8))","stopifnot(sum(is.na(details)) == 2059)","colnames(details) <- c(\"Genus\", \"species\", \"GCminTm\", \"GCmaxTm\", \"GCminBd\", \"GCmaxBd\", \"Toptmin\", \"Toptmax\")","gcT[[\"details\"]] <- details","","gc16S <- read.table(paste(path, \"16S.txt\", sep = \"/\"), sep = \"\\t\", na.string = \"*\")","stopifnot(dim(gc16S) == c(165, 3))","stopifnot(sum(is.na(gc16S)) == 0)","colnames(gc16S) <- c(\"Genus\", \"Topt\", \"GC\")","gcT[[\"gc16S\"]] <- gc16S","","gctRNA <- read.table(paste(path, \"tRNA.txt\", sep = \"/\"), sep = \"\\t\", na.string = \"*\")","stopifnot(dim(gctRNA) == c(51, 3))","stopifnot(sum(is.na(gctRNA)) == 0)","colnames(gctRNA) <- c(\"Genus\", \"Topt\", \"GC\")","gcT[[\"gctRNA\"]] <- gctRNA","","gc23S <- read.table(paste(path, \"23S.txt\", sep = \"/\"), sep = \"\\t\", na.string = \"*\")","stopifnot(dim(gc23S) == c(38, 3))","stopifnot(sum(is.na(gc23S)) == 0)","colnames(gc23S) <- c(\"Genus\", \"Topt\", \"GC\")","gcT[[\"gc23S\"]] <- gc23S","","gc5S <- read.table(paste(path, \"5S.txt\", sep = \"/\"), sep = \"\\t\", na.string = \"*\")","stopifnot(dim(gc5S) == c(71, 3))","stopifnot(sum(is.na(gc5S)) == 0)","colnames(gc5S) <- c(\"Genus\", \"Topt\", \"GC\")","gcT[[\"gc5S\"]] <- gc5S","","gcT[[\"README\"]] <- readLines(paste(path, \"README\", sep = \"/\"))","#Delete forward biblio with encoding problems:","gcT[[\"README\"]] <- gcT[[\"README\"]][-(85:166)]","gcT[[\"README\"]][84] <- \"  Note: this section was deleted on import because of encoding issues.\"","gcT[[\"importgcT\"]] <- readLines(\"importgcT.R\")","","save(gcT, file = \"gcT.rda\")"]}