Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation. (14th December 2010)

• Record Type: Journal Article
• Authors: Garbe, John R.; Elsik, Christine G.; Antoniou, Eric; Reecy, James M.; Clark, Karl J.; Venkatraman, Anand; Kim, Jae-Woo; Schnabel, Robert D.; Michael Dickens, C.; Wolfinger, Russell D.; Fahrenkrug, Scott C.; Taylor, Jeremy F.
• Other Names: Schmutz Sheila M. Academic Editor.
• Is Part Of: Journal of biomedicine and biotechnology. Volume 2010(2010)
• Publication Date: 2010-12-14
• Subjects: Medicine -- Periodicals; Biology -- Periodicals; Biotechnology -- Periodicals; Medicine; Biology; Biotechnology; Médecine; Biologie; Biotechnologie; Biology; Biotechnology; Medicine; Biotechnology; Biomedicine; Electronic journals; Periodical; Periodicals; Electronic journals; 610
• DOI: 10.1155/2010/453638
• Languages: English
• ISSNs: 1110-7243

Abstract

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.