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SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids.

ABSTRACT: 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.

SUBMITTER: Hubert B

PROVIDER: S-EPMC8941118 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids.

Hubert Bert B

Scientific data 20220322 1

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 T ...[more]

PMID: 35318332

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Dataset Information

SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids.

Publications

SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids.

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