Reference:

Description

This track shows the partition of chromosome sequences into fairly homogeneous genome regions or isochores (Bernardi et al., 1985; Bernardi, 2000). Isochore prediction was carried out using IsoFinder (Oliver et al., 2004), a new version of the segmentation algorithm described by Oliver et al (2001, 2002). See also Bernaola-Galván et al (1996, 1999) for further theoretical background. In brief, we move a sliding pointer from left to right along the DNA sequence. At each position of the pointer, we compute the mean G+C values to the left and to the right of the pointer. We then determine the position of the pointer for which the difference between left and right mean values (as measured by the t-statistic) reaches its maximum. Next, we determine the statistical significance of this potential cutting point, after filtering out short-scale heterogeneities below 3 kb by applying a coarse-graining technique. Finally, the program checks whether this significance exceeds a probability threshold. If so, the sequence is cut at this point into two subsequences; otherwise, the sequence remains undivided. The procedure continues recursively for each of the two resulting subsequences created by each cut. This leads to the decomposition of a chromosome sequence into long homogeneous genome regions (LHGRs) with well-defined mean G+C contents, each significantly different from the G+C contents of the adjacent LHGRs. Most LHGRs can be identified with Bernardi's isochores, given their correlation with biological features such as gene, SINE and LINE densities, recombination rate or single nucleotide polymorphism variability (e.g. see Oliver et al 2001, 2002).

Using IsoFinder to find isochores on the Golden Path genome sequences at UCSC

Since IsoFinder can only work with finished sequence, the first task was to locate the islands of Ns in the sequence of each chromosome, then extracting the contigs of finished sequence.

The GC content was used to determine the level of shading in which the isochore is displayed in the Genome Browser. The GC content was transformed in an score in order to enhance the color contrast between different isochores on the screen. The following expression can be used to get the isochore GC content from the score given in data files:

Isochore GC = ((0.35 x score) / 1000) + 0.30

• Bernaola-Galván P, Román-Roldán R, Oliver JL (1996) Compositional segmentation and long-range fractal correlation in DNA sequences. Phys. Rev. E. 53: 5181-5189.
• Bernaola-Galván P, Oliver JL, and Román-Roldán R (1999) Decomposition of DNA sequence complexity. Phys. Rev. Lett. 83: 3336-3339.
• Bernaola-Galván, P., Ivanov, P.Ch., Amaral, L.A.N., Stanley, H.E., 2001. Scale invariance in the nonstationarities of human heart rate. Phys. Rev. Letters 87, 168105.
• Bernardi G, Olofson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. (1985) The Mosaic Genome of Warm-Blooded Vertebrates. Science 228:953-958.
• Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241:3-17.
• Oliver,J. L., P. Bernaola-Galván, P. Carpena and R. Román-Roldán. 2001. Isochore chromosome maps of eukaryotic genomes. GENE 276: 47-56
• Oliver,J.L., P. Carpena, R. Román-Roldán, T. Mata-Balaguer, A. Mejías Romero, Michael Hackenberg and P. Bernaola-Galván. 2002. Isochore chromosome maps of the human genome. GENE 300: 117-127 
• Oliver J.L., P. Carpena, M. Hackenberg, P. Bernaola-Galván. 2004. IsoFinder: computational prediction of isochores in genome sequences. Nucl. Acids. Res. 32: W287-W292. [FREE Full Text] OPEN ACCESS ARTICLE

For isochore maps of other complete eukaryotic genomes, please watch our
On-line Resource on Isochore Mapping

© Jose L. Oliver, 2004 Universidad de Granada, Spain

http://www.ugr.es/~oliver