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Open Access Method

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

Thorsten Schmidt1 and Dmitrij Frishman12*

Author Affiliations

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

2 Institute for Bioinformatics and Systems Biology (MIPS), Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße, D-85764 Neuherberg, Germany

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Genome Biology 2008, 9:R104  doi:10.1186/gb-2008-9-6-r104

Published: 30 June 2008

Additional files

Additional data file 1:

Most borders are shifted between 10 and 100 kb among all methods. No borders are shifted more than 1 Mb in comparison to the BASIO borders. One exception is the least-squares segmentation, which has identical borders with the BASIO map in about 25% of all cases.

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Open Data

Additional data file 2:

For all isochore assignments, more genes reside completely within a single stretch than one would expect by chance. All results are statistically significant (Chi-Square test, all p-values < 0.001).

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Open Data

Additional data file 3:

Analysis of isochore families in all genomes and analysis of differences between methods

Format: PDF Size: 223KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data