m16j {seqinr}

Fragment of the E. coli chromosome

Description

A fragment of the E. coli chromosome that was used in Lobry (1996) to show the change in GC skew at the origin of replication (i.e. the chirochore structure of bacterial chromosomes)

Usage

data(m16j)

Format

A string of 1,616,539 characters

Details

The sequence used in Lobry (1996) was a 1,616,174 bp fragment obtained from the concatenation of nine overlapping sequences (U18997, U00039, L10328, M87049, L19201, U00006, U14003, D10483, D26562. Ambiguities have been resolved since then and its was a chimeric sequence from K-12 strains MG1655 and W3110, the sequence used here is from strain MG1655 only (Blattner et al. 1997).

The chirochore structure of bacterial genomes is illustrated below by a screenshot of a part of figure 1 from Lobry (1996). See the example section to reproduce this figure.

Source

Escherichia coli K-12 strain MG1655. Fragment from U00096 from the EBI Genome Reviews. Acnuc Release 7. Last Updated: Feb 26, 2007. XX DT 18-FEB-2004 (Rel. .1, Created) DT 09-JAN-2007 (Rel. 65, Last updated, Version 70) XX

References

Lobry, J.R. (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Molecular Biology and Evolution, 13:660-665.

F.R. Blattner, G. Plunkett III, C.A. Bloch, N.T. Perna, V. Burland, M. Rilley, J. Collado-Vides, J.D. Glasner, C.K. Rode, G.F. Mayhew, J. Gregor, N.W. Davis, H.A. Kirkpatrick, M.A. Goeden, D.J. Rose, B. Mau, and Y. Shao. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277:1453-1462

citation("seqinr")

Examples

#
# Load data:
#
data(m16j)
#
# Define a function to compute the GC skew:
#
gcskew <- function(x) {
  if (!is.character(x) || length(x) > 1)
  stop("single string expected")
  tmp <- tolower(s2c(x))
  nC <- sum(tmp == "c")
  nG <- sum(tmp == "g")
  if (nC + nG == 0)
  return(NA)
  return(100 * (nC - nG)/(nC + nG))
}
#
# Moving window along the sequence:
#
step <- 10000
wsize <- 10000
starts <- seq(from = 1, to = nchar(m16j), by = step)
starts <- starts[-length(starts)]
n <- length(starts)
result <- numeric(n)
for (i in seq_len(n)) {
  result[i] <- gcskew(substr(m16j, starts[i], starts[i] + wsize - 1))
}
#
# Plot the result:
#
xx <- starts/1000
yy <- result
n <- length(result)
hline <- 0
plot(yy ~ xx, type = "n", axes = FALSE, ann = FALSE, ylim = c(-10, 10))
polygon(c(xx[1], xx, xx[n]), c(min(yy), yy, min(yy)), col = "black", border = NA)
usr <- par("usr")
rect(usr[1], usr[3], usr[2], hline, col = "white", border = NA)
lines(xx, yy)
abline(h = hline)
box()
axis(1, at = seq(0, 1600, by = 200))
axis(2, las = 1)
title(xlab = "position (Kbp)", ylab = "(C-G)/(C+G) [percent]",
 main = expression(paste("GC skew in ", italic(Escherichia~coli))))
arrows(860, 5.5, 720, 0.5, length = 0.1, lwd = 2)
text(860, 5.5, "origin of replication", pos = 4)