Representing GC variation along eukaryotic chromosomes

Jan Pačes, Radek Zíka, Václav Pačes, Adam Pavlíček, Oliver Clay, Giorgio Bernardi

Research output: Contribution to journalArticlepeer-review

30 Scopus citations


Genome sequencing now permits direct visual representation, at any scale, of GC heterogeneity along the chromosomes of several higher eukaryotes. Plots can be easily obtained from the chromosomal sequences, yet sequence releases of mammalian or plant chromosomes still tend to use small scales or window sizes that obscure important large-scale compositional features. To faithfully reveal, at one glance, the compositional variation at a given scale, we have devised a simple scheme that combines line plots with color-coded shading of the regions underneath the plots. The scheme can be applied to different eukaryotic genomes to facilitate their comparison, as illustrated here for a sample of chromosomes chosen from seven selected species. As a complement to a previously published compact view of isochores in the human genome sequence [FEBS Lett. 511 (2002a) 165], we include here an analogous map for the recently sequenced mouse genome, and discuss the contribution of repetitive DNA to the GC variation along the plots. Supplementary information, including a database of color-coded GC profiles for all recently sequenced eukaryotes and the program used to obtain them, are available at

Original languageEnglish (US)
Pages (from-to)135-141
Number of pages7
Issue numberSUPPL.
StatePublished - May 26 2004
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics


Dive into the research topics of 'Representing GC variation along eukaryotic chromosomes'. Together they form a unique fingerprint.

Cite this