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Description of the genome query for

Plot of strand biases

Starting at locus number 1 from the chosen replicon of the chosen genome, we plot locus number versus the cumulative nucleotide bias, either (A-C)/(A+C), (A-G)/(A+G), (A-T)/(A+T), or (G-C)/(G+C). The cumulative nucleotide bias is computed from one strand only, the plus strand as reported to NCBI.

An alternative option is to plot the cumulative locus orientation, where a rightward-oriented ORF has a value of 1, and a leftward-oriented ORF has a value of -1.

Examples:

A very nice example of strand bias exists in the Escherichia coli genome, where there is a sharp cumulative (G-C)/(G+C) minimum at the origin of replication, oriC, and a sharp maximum at the terminus of replication, terC. Selecting instead to plot gene cumulative gene orientation, we see the same trends, but the bias is far less perfect than for cumulative (G-C)/(G+C).
In contrast to example 1 above, the cumulative gene orientation bias in the Bacillus subtilis genome is far sharper. Otherwise, the trends are exactly the same as in Escherichia coli, where the cumulative gene orientation bias and the cumulative (G-C)/(G+C) bias increase away from the origin of DNA replication.

Discussion:

The cumulative (G-C)/(G+C) and the cumulative gene orientation bias are not seen in all of the genomes. We are aware of other oligonucleotide biases that may be more informative than the simple ones that are useful for many bacteria, and these oligonucleotide biases will eventually be incorporated into this query.