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Journal of Biomedicine and Biotechnology
Volume 2010, Article ID 453638, 11 pages
http://dx.doi.org/10.1155/2010/453638
Research Article

Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation

1Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA
2Department of Biology, Georgetown University, Washington, DC 20057, USA
3Department of Animal Sciences, Texas A&M University, College Station, TX 77843, USA
4Division of Animal Science, University of Missouri, Columbia, MO 65211, USA
5Department of Animal Science, Iowa State University, Ames, IA 50011, USA
6Department of Scientific Discovery and Genomics, SAS Institute Inc., Cary, NC 27513, USA

Received 3 September 2010; Accepted 1 November 2010

Academic Editor: Sheila M. Schmutz

Copyright © 2010 John R. Garbe et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The design of oligonucleotide sequences for the detection of gene expression in species with disparate volumes of genome and EST sequence information has been broadly studied. However, a congruous strategy has yet to emerge to allow the design of sensitive and specific gene expression detection probes. This study explores the use of a phylogenomic approach to align transcribed sequences to vertebrate protein sequences for the detection of gene families to design genomewide 70-mer oligonucleotide probe sequences for bovine and porcine. The bovine array contains 23,580 probes that target the transcripts of 16,341 genes, about 72% of the total number of bovine genes. The porcine array contains 19,980 probes targeting 15,204 genes, about 76% of the genes in the Ensembl annotation of the pig genome. An initial experiment using the bovine array demonstrates the specificity and sensitivity of the array.