gcO2: GC content and aerobiosis in bacteria

In seqinr: Biological Sequences Retrieval and Analysis

GC content and aerobiosis in bacteria

Description

This data set was used in Naya et al. (2002) to study the relationship between the genomic G+C content of bacteria and whether they are (stricly) aerobes or anaerobes.

Format

gcO2 is a data frame.

Source

Naya, H., Romero, H., Zavala, A., Alvarez, B. and Musto, H. (2002) Aerobiosis increases the Genomic Guanine Plus Cytosine Content (GC

Data imported into seqinr by J.R. Lobry on 09-OCT-2016. Original source location given in the article was http://oeg.fcien.edu.uy/GCprok/ but is no more active. Data were copied at http://pbil.univ-lyon1.fr/R/donnees/gcO2.txt (cf. section 2.1 in Lobry, J.R (2004) Life history traits and genome structure: aerobiosis and G+C content in bacteria. Lecture Notes in Computer Sciences, 3039:679-686). Import was from this last ressource. There are 130 aerobic genera in this data set while fig. 1 in Naya et al. (2002) gives 126. There is no way to track down the reason for this difference because the original data set was lost (Héctor Musto pers. comm.). The number of anaerobic genera (n = 69) is consistent between the present data set and fig. 1 in Naya et al. (2002).

References

citation("seqinr")

Examples

data(gcO2)

seqinr documentation built on March 31, 2023, 3:05 p.m.