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Dog Genome Sequencing

A Survey of Canine Expressed Sequence Tags and a Display of Their Annotations Through a Flexible Web-Based Interface

L. E. Palmer, A. L. O'Shaughnessy, R. R. Preston, L. Santos, V. S. Balija, L. U. Nascimento, T. L. Zutavern, P. S. Henthorn, G. J. Hannon, and W. R. McCombie

From the Cold Spring Harbor Laboratory, Genome Research Center, 500 Sunnyside Blvd., Woodbury, NY 11797 (Palmer, O'Shaughnessy, Preston, Santos, Balija, Nascimento, Zutavern, and McCombie); the Department of Clinical Studies, University of Pennsylvania, School of Veterinary Medicine, 3900 Delancey St., Philadelphia, PA 19104-6010 (Henthorn); and Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, NY 11724 (Hannon).

Address correspondence to W. R. McCombie at the address above, or e-mail: mccombie@cshl.org.

We have initially sequenced approximately 8,000 canine expressed sequence tags (ESTs) from several complementary DNA (cDNA) libraries: testes, whole brain, and Madin-Darby canine kidney (MDCK) cells. Analysis of these sequences shows that they provide partial sequence information for about 5%–10% of the canine genes. An analysis pipeline has been created to cluster the ESTs and to map individual ESTs as well as clustered ESTs to both the human genome and the human proteome. Gene ontology (GO) terms have been assigned to the ESTs and clusters based on their top matches to the International Protein Index (IPI) set of human proteins. The data generated is stored in a MySQL relational database for analysis and display. A Web-based Perl script has been written to display the analyzed data to the scientific community.

EST Sequencing

The following ESTs were sequenced from 3 different non-normalized cDNA libraries:

  • 594 mdck cell ESTs were submitted on May 12, 2000.  GB Accession numbers  AW784161 - AW784754.

  • 133 mdck cell ESTs were submitted on November 14, 2000.  GB Accession numbers BF228906 - BF229037.

  • 80 testes ESTs were submitted on November 14, 2000.  GB Accession numbers BF228826 - BF228905.

  • 4747 testes ESTs were submitted on February 18, 2002.  GB Accession numbers BN536501 - BN541247.

  • 1976 brain ESTs were submitted on May 2, 2002.  GB Accession numbers BQ233922 - BQ235897.

  • 627 brain ESTs were submitted on May 13, 2002.  GB Accession numbers BQ289787 - BQ290413.

  • 316 brain ESTs were submitted on July 25, 2002.  GB Accession numbers BQ788209 - BQ788524.

These sequences are also available via ftp.

Additional sets of ESTs are being sequenced from these libraries at CSHL.  The working versions of those sequences, if available, can be found here via FTP.  Sequences will be trimmed of vector and checked for minimum quality before submission.

BLAST Search

Search against the dog ESTs contained on our site.

EST Annotations

Thanks to the CANINE HEALTH FOUNDATION for their support in this project.

Last updated: 23 April 2003
Questions? Contact Dick McCombie