SkewDB

doi:10.5061/dryad.g4f4qrfr6
Last database update: 21st of October 2021

Welcome to SkewDB! A free database of GC and many other skews for over 30,200 chromosomes and plasmids (preprint, blog post).

Scatter plot of observed GC skew levels (y axis) and a calculated predictor (x axis)

Scatter plot of observed GC skew levels (y axis) and a calculated predictor (x axis)

This database is created by the open source Antonie software, based on public DNA sequence, annotation and taxonomic data as gathered from NCBI data.

In addition, for all 28000 chromosomes and plasmids, individual files are available that show all the various skews with 4096-nucleotide granularity. This is good for creating plots or studying local chromosome behaviour.

Cumulative GC skew for C. difficile

Cumulative GC skew for C. difficile

Here are the relevant files:

You can also query the database directly here.

SkewDB was created by bert hubert based on public DNA sequence, annotation and taxonomic data. It is wonderful that all this data is available. The hope is that SkewDB can support further research into chromosomes showing GC skew.

If you’ve been able to benefit from SkewDB data, please do find a way to cite the project. The preprint that describes the data is also on BioRxiv, it can be cited as:

SkewDB: A comprehensive database of GC and 10 other skews for over 28,000 chromosomes and plasmids
Bert Hubert
bioRxiv 2021.09.09.459602; doi: https://doi.org/10.1101/2021.09.09.459602

The database itself also has a doi, doi:10.5061/dryad.g4f4qrfr6.

Some informal background is available in these three blog posts.

Meanwhile do contact me on bert@hubertnet.nl if you have any questions!

Contents

Here is what you’ll find in the SkewDB. Fields that have no description should be ignored, unless you want to delve into the source to find out what they are. Also consult the preprint.

name NZ_CP019870.1 Sequence identifier
fullname NZ_CP019870.1 Clostridioides difficile strain BR81 chromosome, complete genome Full name
acount 1468605 Number of A nucleotides in chromosome
ccount 595727 Number of C nucleotides in chromosome
gcount 588291 Number of G nucleotides in chromosome
tcount 1471761 Number of T nucleotides in chromosome
realm1 Bacteria Taxonomic data
realm2 Terrabacteria group Taxonomic data
realm3 Firmicutes Taxonomic data
realm4 Clostridia Taxonomic data
realm5 Clostridiales Taxonomic data
flipped 0 If this genome was 'flipped' because it was sequenced in the "wrong" order
siz 4124383 Number of nucleotides in chromosome
gccount 1184018 Number of GC nucleotides in chromosome
ngcount 684359 Number of non-coding nucleotides in chromosome
acounts2 474821 Number of A nucleotides in the 3rd codon position
ccounts2 101127 Number of C nucleotides in the 3rd codon position
gcounts2 100290 Number of G nucleotides in the 3rd codon position
tcounts2 470372 Number of T nucleotides in the 3rd codon position
alpha1gc 0.06388 Gradient of G excess compared to C on leading strand
alpha2gc 0.063053 Gradient of C excess compared to G on lagging strand
shift -47650 How far the chromosome had to be rotated to start at the Origin of replication
div 0.489762 Ratio of sizes of leading and lagging strands
alpha1ta -0.064201 Gradient of T excess compared to A on leading strand
alpha2ta -0.066181 Gradient of A excess compared to T on lagging strand
alpha1sb 0.582759 Gradient of gene excess on leading strand
alpha2sb 0.595694 Gradient of gene excess on lagging strand (same sign)
alpha1gc0 0.044523 Excess of G over C in the first coding codon position on leading strand. Detrended, so the codon bias has been subtracted
alpha2gc0 0.046124 Excess of C over G in the first coding codon position on lagging strand. Detrended, so the codon bias has been subtracted
alpha1gc1 -0.00456 Same, second codon position
alpha2gc1 -0.004271 Same, second codon position
alpha1gc2 0.013686 Same, third codon position
alpha2gc2 0.014115 Same, third codon position
alpha1ta0 -0.034711 Excess of T over A in the first coding codon position on leading strand. Detrended, so the codon bias has been subtracted
alpha2ta0 -0.035573 Excess of A over T in the first coding codon position on lagging strand. Detrended, so the codon bias has been subtracted
alpha1ta1 -0.007392 Same, second codon position
alpha2ta1 -0.008421 Same, second codon position
alpha1ta2 -0.014013 Same, third codon position
alpha2ta2 -0.015103 Same, third codon position
alpha1gcNG 0.008434 Excess of G over C in non-coding nucleotides on the leading strand
alpha2gcNG 0.008888 Excess of C over G in non-coding nucleotides on the lagging strand
alpha1taNG -0.007312 Excess of T over A in non-coding nucleotides on the leading strand
alpha2taNG -0.007842 Excess of A over T in non-coding nucleotides on the lagging strand
rmsGC 0.000818 Relative Root Mean Square error of fit. This is per nucleotide and scaled. 0.000818 represents on average a 0.08% error, per nucleotide position
rmsTA 0.001317
rmsSB 0.00128
rmsGC0 0.001125
rmsGC1 0.003669
rmsGC2 0.000957
rmsTA0 0.001566
rmsTA1 0.002921
rmsTA2 0.002964
rmsGCNG 0.00211
rmsTANG 0.002764
gccontent 0.287078 GC fraction of chromosome
ggcfrac 0.626893
cgcfrac 0.373107
ttafrac 0.438995
atafrac 0.561005
gfrac 0.188601 Which fraction of coding nucleotides ("genes") is G
cfrac 0.11225 Which fraction of coding nucleotides ("genes") is C
tfrac 0.306923 Which fraction of coding nucleotides ("genes") is T
afrac 0.392226 Which fraction of coding nucleotides ("genes") is A
leadafrac 0.392415
leadcfrac 0.11233
leadgfrac 0.187254
leadtfrac 0.308
lagafrac 0.391272
lagcfrac 0.112402
laggfrac 0.189846
lagtfrac 0.30648