gcT {seqinr}

GC content and temperature in bacteria

Description

This data set was used in Galtier and Lobry (1997) to study the relationship between the optimal growth temperature of bacteria and their G+C content at the genomic level and locally were selection is active to maintain secondary structures in the stems of RNAs.

Format

gcT is a list containing the 9 following components:

species

is a data frame containing the optimal growth temperature and genomic G+C content for 772 bacterial species. Detailled explanations for this table and the following are available in the README component.

genus

is a data frame containing the optimal growth temperature and genomic G+C content for 224 bacterial genus.

details

is a data frame with more information, see README.

gc16S

is a data frame containing the optimal growth temperature and stems G+C content for 16S RNA from 165 bacterial genus.

gctRNA

is a data frame containing the optimal growth temperature and stems G+C content for tRNA from 51 bacterial genus.

gc23S

is a data frame containing the optimal growth temperature and stems G+C content for 23S RNA from 38 bacterial genus.

gc5S

is a data frame containing the optimal growth temperature and stems G+C content for 5S RNA from 71 bacterial genus.

README

is the original README file from ftp://biom3.univ-lyon1.fr/pub/datasets/JME97/ last updated 13-MAY-2002.

importgcT

is the R script used to import data.

Source

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.

Data imported into seqinr with the R script given in the last component of the dataset by J.R. Lobry on 09-OCT-2016.

References

citation("seqinr")

Examples

data(gcT)