NAR Molecular Biology Database Collection entry number 598

http://projects.tcag.ca/xenodup/

Cheung J., Zhang J., Khaja R., MacDonald J.R. and Scherer S.W.

Program in Genetics and Genomic Biology, The Hospital for Sick Children, 555 University Ave, Toronto ON Canada M5G 1X8

Contact jeffm@genet.sickkids.on.ca

This web site contains information about segmental duplications in the genomes of mouse, dog chicken and rat. Information about segmental duplication in the human genome is presented at http://projects.tcag.ca/humandup. Analyses based on previous genome assemblies can be found in the Previous Analyses section.

The criteria used to identify regions of segmental duplication are as follows:
- Sequence identity of at least 90%
-Sequence length of at least 5 kb
-Not be entirely composed of repetitive elements

The segmental duplication data and summary statistics are available for download in the Data section. Publications and their supplementary materials can be accessed in the Publications section. The segmental duplication data can be visualized in a genome browser in the GBrowse section. Selected annotation tracks (except the segmental duplication track) have also been obtained from UCSC and loaded into the genome browser. Detailed information (e.g. overlapping genes, overlapping clones, detailed alignment) can be obtained by clicking on a duplication cluster in GBrowse. Both keyword search and BLAT search are available from the Home page.

The Non-Human Genome Segmental Duplication Database is continually updated, including the archived copies of the analysis of all previous genome assemblies, and will include all new species as they become available.

We thank The Centre for Applied Genomics at the Hospital for Sick Children (HSC) as well as collaborators worldwide. Supported by Genome Canada, the Howard Hughes Medical Institute International Scholar Program (to S.W.S.) and the HSC Foundation.

1. Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 2003;4(4):R25. Epub 2003 Mar 17.
2. Armengol L, Pujana MA, Cheung J, Scherer SW, Estivill X. Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum Mol Genet. 2003 Sep 1;12(17):2201-8. Epub 2003 Jul 08.
3. Scherer SW, Cheung J, MacDonald JR, et al. Human chromosome 7: DNA sequence and biology. Science. 2003 May 2;300(5620):767-72. Epub 2003 Apr 10.
4. Gimelli G, Pujana MA, Patricelli MG, Russo S, Giardino D, Larizza L, Cheung J, Armengol L, Schinzel A, Estivill X, Zuffardi O. Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet. 2003 Apr 15;12(8):849-58.
5. Estivill X, Cheung J, Pujana MA, Nakabayashi K, Scherer SW, Tsui LC. Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome. Hum Mol Genet. 2002 Aug 15;11(17):1987-95.
6: Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, Heng HH, Koop BF, Scherer SW. Recent segmental and gene duplications in the mouse genome. Genome Biol. 2003;4(8):R47. Epub 2003 Jul 09.

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