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

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2010-01-01
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Garbe, John
Elsik, Christine
Antoniou, Eric
Reecy, James
Clark, Karl
Venkatraman, Anand
Kim, Jae-Woo
Schnabel, Robert
Dickens, C. Michael
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Animal Science
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.

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This article is from Journal of Biomedicine and Biotechnology 2010 (2010): 453638, doi:10.1155/2010/453638. Posted with permission.

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Fri Jan 01 00:00:00 UTC 2010
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