Identifying repeat domains in large genomes

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Degui Zhi¹ , Benjamin J Raphael² , Alkes L Price³ , Haixu Tang⁴ and Pavel A Pevzner²

¹Bioinformatics Program, University of California, San Diego, CA 92093-0419, USA

²Department of Computer Science and Engineering, University of California, San Diego, CA 92093-0114, USA

³Department of Genetics, Harvard Medical School, Boston, MA 02115, USA

⁴School of Informatics and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47408, USA

author email corresponding author email

Genome Biology 2006, 7:R7doi:10.1186/gb-2006-7-1-r7


Published:	31 January 2006

Subject areas: Bioinformatics, Evolution

Additional File 1:

A zipped file of browsable HTML files with a complete list of the connected components in the repeat domain graph of human Repbase.

Format: GZ Size: 2.1MB Download file

Additional File 2:

The full version of Table 1. The list is sorted by the total length of shared domains.

Format: XLS Size: 30KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 3:

Labeling follows that of Figure 2b. The three Y-forks are highlighted green.

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Additional File 4:

An analysis of the comparative repeat domain graph from mouse and rat RepeatScout repeat libraries.

Format: DOC Size: 1.2MB Download file

This file can be viewed with: Microsoft Word Viewer

Additional File 5:

An example of how palindromic sequences are handled by our revised algorithm.

Format: DOC Size: 142KB Download file

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Additional File 6:

Modified ABA program and the perl scripts used for analyzing the repeat domain graphs.

Format: TAR Size: 60KB Download file