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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.

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GC differences between neighboring isochores. The distribution of GC differences between adjacent isochores is shown for each method. The thick bars within each box plot indicate the median. The IsoFinder and GC-Profile assignments have the largest GC deltas, on average, whereas in the BASIO isochore map the GC deltas are lowest (median 3.5, mean 4.0). Outliers are not shown in this plot. The average delta GC in the consensus map is 4.6, the median 4.1.
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Figure 2: GC differences between neighboring isochores. The distribution of GC differences between adjacent isochores is shown for each method. The thick bars within each box plot indicate the median. The IsoFinder and GC-Profile assignments have the largest GC deltas, on average, whereas in the BASIO isochore map the GC deltas are lowest (median 3.5, mean 4.0). Outliers are not shown in this plot. The average delta GC in the consensus map is 4.6, the median 4.1.

Mentions: Using the GC level of each isochore, we evaluated the GC difference (delta GC) between adjacent segments and found that the delta GC distributions of the compared methods are significantly different. The BASIO and the least-squares data show the smallest GC jumps while the GC-Profile and IsoFinder methods produce the broadest distribution and the greatest delta GC values on average (Figure 2). One explanation for this may be that short isochores are more likely to model local GC outliers, which results in higher delta GC differences between adjacent segments, on average.


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

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

GC differences between neighboring isochores. The distribution of GC differences between adjacent isochores is shown for each method. The thick bars within each box plot indicate the median. The IsoFinder and GC-Profile assignments have the largest GC deltas, on average, whereas in the BASIO isochore map the GC deltas are lowest (median 3.5, mean 4.0). Outliers are not shown in this plot. The average delta GC in the consensus map is 4.6, the median 4.1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: GC differences between neighboring isochores. The distribution of GC differences between adjacent isochores is shown for each method. The thick bars within each box plot indicate the median. The IsoFinder and GC-Profile assignments have the largest GC deltas, on average, whereas in the BASIO isochore map the GC deltas are lowest (median 3.5, mean 4.0). Outliers are not shown in this plot. The average delta GC in the consensus map is 4.6, the median 4.1.
Mentions: Using the GC level of each isochore, we evaluated the GC difference (delta GC) between adjacent segments and found that the delta GC distributions of the compared methods are significantly different. The BASIO and the least-squares data show the smallest GC jumps while the GC-Profile and IsoFinder methods produce the broadest distribution and the greatest delta GC values on average (Figure 2). One explanation for this may be that short isochores are more likely to model local GC outliers, which results in higher delta GC differences between adjacent segments, on average.

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