Limits...
Assignment of isochores for all completely sequenced vertebrate genomes using a consensus.

Schmidt T, Frishman D - Genome Biol. (2008)

Bottom Line: We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution.We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, D-85350 Freising, Germany.

ABSTRACT
We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution. We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

Show MeSH

Related in: MedlinePlus

Comparison of isochore assignments in the human genome made by the different methods. All isochore maps show remarkable differences with respect to the number and the average length of their isochore segments. The IsoFinder and BASIO methods result in the most fine-grained segmentations while GC-Profile and least-squares produce less fragmented partitioning of the genome. The consensus map provides a compromise solution. (a) Number of isochore stretches. (b) Average isochore length.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2481423&req=5

Figure 1: Comparison of isochore assignments in the human genome made by the different methods. All isochore maps show remarkable differences with respect to the number and the average length of their isochore segments. The IsoFinder and BASIO methods result in the most fine-grained segmentations while GC-Profile and least-squares produce less fragmented partitioning of the genome. The consensus map provides a compromise solution. (a) Number of isochore stretches. (b) Average isochore length.

Mentions: Published isochore datasets show remarkable diversity. In the following we will use the human genome for comparisons of different isochore assignments if not stated otherwise. The number of isochore segments found in the human genome ranges from about 1,200 for GC-Profile to up to more than 76,000 for BASIO. As a consequence, the resulting isochores show very different length distributions. Isochores discovered by least-squares segmentation are the longest at an average of 2,459 kb, whereas BASIO and IsoFinder segments are the shortest at an average of 40 and 72 kb, respectively (Figure 1). It can be seen that IsoFinder and BASIO are clearly in a different league compared to GC-Profile and least-squares in terms of the number and average length of isochores. This divergence results from different criteria used by the four tested methods to determine the beginning and end of the segments, and the window lengths of 10 and 100 kb used by BASIO and least-squares, respectively. As explained in Materials and methods, a difficult challenge in GC-content-based partitioning of complex eukaryotic genomes is to find a set of parameters suitable for coping with the significantly different levels of GC fluctuations in the GC-rich and GC-poor regions.


Assignment of isochores for all completely sequenced vertebrate genomes using a consensus.

Schmidt T, Frishman D - Genome Biol. (2008)

Comparison of isochore assignments in the human genome made by the different methods. All isochore maps show remarkable differences with respect to the number and the average length of their isochore segments. The IsoFinder and BASIO methods result in the most fine-grained segmentations while GC-Profile and least-squares produce less fragmented partitioning of the genome. The consensus map provides a compromise solution. (a) Number of isochore stretches. (b) Average isochore length.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2481423&req=5

Figure 1: Comparison of isochore assignments in the human genome made by the different methods. All isochore maps show remarkable differences with respect to the number and the average length of their isochore segments. The IsoFinder and BASIO methods result in the most fine-grained segmentations while GC-Profile and least-squares produce less fragmented partitioning of the genome. The consensus map provides a compromise solution. (a) Number of isochore stretches. (b) Average isochore length.
Mentions: Published isochore datasets show remarkable diversity. In the following we will use the human genome for comparisons of different isochore assignments if not stated otherwise. The number of isochore segments found in the human genome ranges from about 1,200 for GC-Profile to up to more than 76,000 for BASIO. As a consequence, the resulting isochores show very different length distributions. Isochores discovered by least-squares segmentation are the longest at an average of 2,459 kb, whereas BASIO and IsoFinder segments are the shortest at an average of 40 and 72 kb, respectively (Figure 1). It can be seen that IsoFinder and BASIO are clearly in a different league compared to GC-Profile and least-squares in terms of the number and average length of isochores. This divergence results from different criteria used by the four tested methods to determine the beginning and end of the segments, and the window lengths of 10 and 100 kb used by BASIO and least-squares, respectively. As explained in Materials and methods, a difficult challenge in GC-content-based partitioning of complex eukaryotic genomes is to find a set of parameters suitable for coping with the significantly different levels of GC fluctuations in the GC-rich and GC-poor regions.

Bottom Line: We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution.We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, D-85350 Freising, Germany.

ABSTRACT
We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution. We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

Show MeSH
Related in: MedlinePlus