A Color Visualization Method to the Isochores of DNA Sequences

Isochore is one of the most striking features of the DNA sequences of warm-blooded animals. Isochores affect both coding and non-coding sequences and reflect a fundamental level of genome organization. In this paper, a new method (GCDT) is introduced to display the isochore structures. This method not only can illustrate the isochore structures very well, but also can provide a more detailed description about the GC variation along the genome sequence. GCDT gives an intuitive visual description for the DNA sequences, and matches well with the results of z' curve.

[1]  Ramón Román-Roldán,et al.  Isochore chromosome maps of the human genome. , 2002, Gene.

[2]  Feng Gao,et al.  Isochore structures in the chicken genome , 2006, The FEBS journal.

[3]  Feng Gao,et al.  GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences , 2006, Nucleic Acids Res..

[4]  Laurence H Pearl,et al.  Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2. , 2002, Nucleic acids research.

[5]  Ren Zhang,et al.  Isochore structures in the mouse genome. , 2004, Genomics.

[6]  Michael Hackenberg,et al.  IsoFinder: computational prediction of isochores in genome sequences , 2004, Nucleic Acids Res..

[7]  Xuemei Deng,et al.  Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes , 2007, BMC Evolutionary Biology.

[8]  Dan Graur,et al.  GC composition of the human genome: in search of isochores. , 2005, Molecular biology and evolution.

[9]  Ivo Grosse,et al.  Applications of Recursive Segmentation to the Analysis of DNA Sequences , 2002, Comput. Chem..

[10]  R Zhang,et al.  A Novel Method to Calculate the G+C Content of Genomic DNA Sequences , 2001, Journal of biomolecular structure & dynamics.

[11]  Giorgio Bernardi,et al.  An isochore map of human chromosomes. , 2006, Genome research.

[12]  P Bernaola-Galván,et al.  Isochore chromosome maps of eukaryotic genomes. , 2001, Gene.

[13]  G Bernardi,et al.  An approach to the organization of eukaryotic genomes at a macromolecular level. , 1976, Journal of molecular biology.