## File: chargaff.Rd

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r-cran-seqinr 3.4-5-2
 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131 \name{chargaff} \alias{chargaff} \docType{data} \title{Base composition in ssDNA for 7 bacterial DNA} \description{ Long before the genomic era, it was possible to get some data for the global composition of single-stranded DNA chromosomes by direct chemical analyses. These data are from Chargaff's lab and give the base composition of the L (Ligth) strand for 7 bacterial chromosomes. } \usage{data(chargaff)} \format{ A data frame with 7 observations on the following 4 variables. \describe{ \item{[A]}{frequencies of A bases in percent} \item{[G]}{frequencies of G bases in percent} \item{[C]}{frequencies of C bases in percent} \item{[T]}{frequencies of T bases in percent} } } \details{ Data are from Table 2 in Rudner \emph{et al.} (1969) for the L-strand. Data for \emph{Bacillus subtilis} were taken from a previous paper: Rudner \emph{et al.} (1968). This is in fact the average value observed for two different strains of \emph{B. subtilis}: strain W23 and strain Mu8u5u16.\cr Denaturated chromosomes can be separated by a technique of intermitent gradient elution from a column of methylated albumin kieselguhr (MAK), into two fractions, designated, by virtue of their buoyant densities, as L (light) and H (heavy). The fractions can be hydrolyzed and subjected to chromatography to determined their global base composition.\cr The surprising result is that we have almost exactly A=T and C=G in single stranded-DNAs. The second paragraph page 157 in Rudner \emph{et al.} (1969) says: "Our previous work on the complementary strands of \emph{B. subtilis} DNA suggested an additional, entirely unexpected regularity, namely, the equality in either strand of 6-amino and 6-keto nucleotides ( A + C = G + T). This relationship, which would normally have been regarded merely as the consequence of base-pairing in DNA duplex and would not have been predicted as a likely property of a single strand, is shown here to apply to all strand specimens isolated from denaturated DNA of the AT type (Table 2, preps. 1-4). It cannot yet be said to be established for the DNA specimens from the equimolar and GC types (nos. 5-7)." Try \code{example(chargaff)} to mimic figure page 17 in Lobry (2000) : \if{html}{\figure{chargaff.png}{options: width=400}} \if{latex}{\figure{chargaff.png}{options: width=12cm}} Note that \code{example(chargaff)} gives more details: the red areas correspond to non-allowed values beause the sum of the four bases frequencies cannot exceed 100\%. The white areas correspond to possible values (more exactly to the projection from \code{R^4} to the corresponding \code{R^2} planes of the region of allowed values). The blue lines correspond to the very small subset of allowed values for which we have in addition PR2 state, that is \code{[A]=[T]} and \code{[C]=[G]}. Remember, these data are for ssDNA! } \source{ Rudner, R., Karkas, J.D., Chargaff, E. (1968) Separation of \emph{B. subtilis} DNA into complementary strands, III. Direct Analysis. \emph{Proceedings of the National Academy of Sciences of the United States of America}, \bold{60}:921-922.\cr Rudner, R., Karkas, J.D., Chargaff, E. (1969) Separation of microbial deoxyribonucleic acids into complementary strands. \emph{Proceedings of the National Academy of Sciences of the United States of America}, \bold{63}:152-159.\cr } \references{ Lobry, J.R. (2000) The black hole of symmetric molecular evolution. Habilitation thesis, Université Claude Bernard - Lyon 1. \url{https://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf}. \code{citation("seqinr")} } \examples{ data(chargaff) op <- par(no.readonly = TRUE) par(mfrow = c(4,4), mai = rep(0,4), xaxs = "i", yaxs = "i") xlim <- ylim <- c(0, 100) for( i in 1:4 ) { for( j in 1:4 ) { if( i == j ) { plot(chargaff[,i], chargaff[,j],t = "n", xlim = xlim, ylim = ylim, xlab = "", ylab = "", xaxt = "n", yaxt = "n") polygon(x = c(0, 0, 100, 100), y = c(0, 100, 100, 0), col = "lightgrey") for( k in seq(from = 0, to = 100, by = 10) ) { lseg <- 3 segments(k, 0, k, lseg) segments(k, 100 - lseg, k, 100) segments(0, k, lseg, k) segments(100 - lseg, k, 100, k) } string <- paste(names(chargaff)[i],"\n\n",xlim[1],"\% -",xlim[2],"\%") text(x=mean(xlim),y=mean(ylim), string, cex = 1.5) } else { plot(chargaff[,i], chargaff[,j], pch = 1, xlim = xlim, ylim = ylim, xlab = "", ylab = "", xaxt = "n", yaxt = "n", cex = 2) iname <- names(chargaff)[i] jname <- names(chargaff)[j] direct <- function() segments(0, 0, 50, 50, col="blue") invers <- function() segments(0, 50, 50, 0, col="blue") PR2 <- function() { if( iname == "[A]" & jname == "[T]" ) { direct(); return() } if( iname == "[T]" & jname == "[A]" ) { direct(); return() } if( iname == "[C]" & jname == "[G]" ) { direct(); return() } if( iname == "[G]" & jname == "[C]" ) { direct(); return() } invers() } PR2() polygon(x = c(0, 100, 100), y = c(100, 100, 0), col = "pink4") polygon(x = c(0, 0, 100), y = c(0, 100, 0)) } } } # Clean up par(op) } \keyword{datasets}