chargaff(seqinr)
chargaff()所属R语言包：seqinr
Base composition in ssDNA for 7 bacterial DNA
7细菌DNA的单链DNA的碱基组成
译者：生物统计家园网 机器人LoveR
描述----------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.
龙前基因组时代，它是可能的，通过直接的化学分析的全球组合物，单链DNA的染色体获得的一些数据。这些数据从查加夫的实验室和得到的基料组合物的L（Ligth）链7细菌的染色体。
用法----------Usage----------
data(chargaff)
格式----------Format----------
A data frame with 7 observations on the following 4 variables.
一种数据框与7上的以下4个变量的观察。
[A] frequencies of A bases in percent
[A]一个碱基在频率％
[G] frequencies of G bases in percent
[G] G碱基的频率％
[C] frequencies of C bases in percent
[C]频率的C碱基％
[T] frequencies of T bases in percent
[T] T碱基频率％
Details
详细信息----------Details----------
Data are from Table 2 in Rudner et al. (1969) for the L-strand. Data for Bacillus subtilis were taken from a previous paper: Rudner et al. (1968). This is in fact the average value observed for two different strains of B. subtilis: strain W23 and strain Mu8u5u16.<br> 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.<br> 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 et al. (1969) says: "Our previous work on the complementary strands of 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)."
数据是从表2在鲁德纳等。 （1969）的L链。枯草芽孢杆菌的数据是从以前的文件：鲁德纳等。 （1968）。这是在实际上的平均值，观察到两种不同的菌株枯草芽孢杆菌：应变W23和应变Mu8u5u16。<br>文章改性的染色体，可以从一列的甲基化白蛋白硅藻土（MAK），进入间歇性梯度洗脱的技术分离两个馏分，指定，凭借其浮力密度，为L（光）和H（重）。馏分，则可水解，并进行色谱分离，以确定他们在全球的碱基组成。<BR>令人惊讶的结果是，我们有几乎一模一样A = T，C = G的单链DNA片段。鲁德纳等第二段第157页。 （1969年）说：“我们以前的工作建议枯草芽孢杆菌的DNA互补链的一个额外的，完全没有预料到的规律性，即，平等，无论是链6 - 氨基和6 - 酮核苷酸（A + C = G + T）。这种关系，通常被视为仅仅是作为双链DNA碱基配对的结果，也不会被预测的单链作为一个可能的财产，适用于所有股标本分离出DNA的变性AT型（表2，税号1-4）。它尚未可以说要建立从等摩尔和GC的类型（编号5-7）的DNA试样“。
源----------Source----------
Rudner, R., Karkas, J.D., Chargaff, E. (1968) Separation of B. subtilis DNA into complementary strands, III. Direct Analysis. Proceedings of the National Academy of Sciences of the United States of America, 60:921-922.<br> Rudner, R., Karkas, J.D., Chargaff, E. (1969) Separation of microbial deoxyribonucleic acids into complementary strands. Proceedings of the National Academy of Sciences of the United States of America, 63:152-159.
鲁德纳，R.，Karkas，JD，查加夫，E.（1968）分离的枯草芽孢杆菌的DNA互补链，III。直接分析。论文集国家科学院美利坚合众国，60:921-922。参考鲁德纳，R.，Karkas，JD，查加夫，E.（1969）分离到的微生物的脱氧核糖核酸互补链。诉讼的美国国家科学院的美利坚合众国，63:152-159。
参考文献----------References----------
http://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf. 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</code> to the corresponding <code>R^2</code> 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]</code> and <code>[C]=[G]</code>. Remember, these data are for ssDNA !
实例----------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[清理]
par(op)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-9-30 01:14:52
