AHU Holding Research, Nootdorp, Netherlands.
Sci Data. 2022 Mar 22;9(1):92. doi: 10.1038/s41597-022-01179-8.
GC skew denotes the relative excess of G nucleotides over C nucleotides on the leading versus the lagging replication strand of eubacteria. While the effect is small, typically around 2.5%, it is robust and pervasive. GC skew and the analogous TA skew are a localized deviation from Chargaff's second parity rule, which states that G and C, and T and A occur with (mostly) equal frequency even within a strand. Different bacterial phyla show different kinds of skew, and differing relations between TA and GC skew. This article introduces an open access database ( https://skewdb.org ) of GC and 10 other skews for over 30,000 chromosomes and plasmids. Further details like codon bias, strand bias, strand lengths and taxonomic data are also included. The SkewDB can be used to generate or verify hypotheses. Since the origins of both the second parity rule and GC skew itself are not yet satisfactorily explained, such a database may enhance our understanding of prokaryotic DNA.
GC 倾斜表示在原核生物的先导链与滞后链上,G 核苷酸相对于 C 核苷酸的相对过剩。虽然这种效应很小,通常在 2.5%左右,但它是稳健且普遍存在的。GC 倾斜和类似的 TA 倾斜是Chargaff 第二碱基配对规则的局部偏离,该规则指出,即使在一个链内,G 和 C 以及 T 和 A 的出现频率(大部分)相等。不同的细菌门显示出不同类型的倾斜,以及 TA 和 GC 倾斜之间的不同关系。本文介绍了一个开放获取的数据库(https://skewdb.org),其中包含超过 30000 个染色体和质粒的 GC 和其他 10 种倾斜。还包括了进一步的细节,如密码子偏向性、链偏向性、链长和分类学数据。SkewDB 可用于生成或验证假设。由于第二碱基配对规则和 GC 倾斜本身的起源尚未得到令人满意的解释,因此这样的数据库可能会增强我们对原核 DNA 的理解。