Compositional segments in Cyanobacteria

DNA sequences are formed by patches or domains of different nucleotide composition. In simple, homegeneous sequences, domains can be identified by eye; however, most DNA sequences show a complex compositional heterogeneity. We used a computationally efficient segmentation method to analyse such non-stationary sequence structures, based on the Jensen–Shannon entropic divergence (Bernaola-Galván et al., 2012; Oliver et al., 1999).

We divide a DNA sequence into compositionally homogeneous segments (domains) by iterating a local optimization procedure at a given statistical significance. Once a sequence is partitioned into domains, a global measure of sequence compositional complexity (SCC), accounting for both the sizes and compositional biases of all the segments in the sequence can be derived (Román-Roldán et al., 1998). SCC is computed as a function of the significance level, which provides a multiscale view of sequence complexity. Four DNA alphabets or mapping rules (Bernaola-Galván et al., 1999) were used: {A,T,C,G}, {S,W}, {R,Y} and {K,M}.

Using the UCSC Genome Browser, we provide below links to genome maps of the compositional domains obtained at the 0.95 significance level in species of Cyanobacteria.

Note that, once at UCSC Genome Browser, you can obtain a complete list of segment coordinates in plain text by clicking on Tools --> Table Browser.

References

Genome maps of compositional segments at UCSC: