Table of Contents Author Guidelines Submit a Manuscript
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.

Linked References

  1. S. Kumar and S. B. Hedges, “A molecular timescale for vertebrate evolution,” Nature, vol. 392, no. 6679, pp. 917–920, 1998. View at Publisher · View at Google Scholar · View at Scopus
  2. S. P. Suchyta, S. Sipkovsky, R. Kruska et al., “Development and testing of a high-density cDNA microarray resource for cattle,” Physiological Genomics, vol. 15, no. 2, pp. 158–164, 2004. View at Google Scholar · View at Scopus
  3. S. H. Zhao, J. Recknor, J. K. Lunney et al., “Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig,” Genomics, vol. 86, no. 5, pp. 618–625, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. X. Li, Z. He, and J. Zhou, “Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation,” Nucleic Acids Research, vol. 33, no. 19, pp. 6114–6123, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. Y. Liu, X. Qin, X. Z. H. Song et al., “Bos taurus genome assembly,” BMC Genomics, vol. 10, article 180, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. J. P. Steibel, M. Wysocki, J. K. Lunney et al., “Assessment of the swine protein-annotated oligonucleotide microarray,” Animal Genetics, vol. 40, no. 6, pp. 883–893, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. M. S. Boguski, T. M. J. Lowe, and C. M. Tolstoshev, “dbEST—database for 'expressed sequence tags',” Nature Genetics, vol. 4, no. 4, pp. 332–333, 1993. View at Publisher · View at Google Scholar · View at Scopus
  8. A. Morgulis, E. M. Gertz, A. A. Schäffer, and R. Agarwala, “A fast and symmetric DUST implementation to mask low-complexity DNA sequences,” Journal of Computational Biology, vol. 13, no. 5, pp. 1028–1040, 2006. View at Publisher · View at Google Scholar · View at Scopus
  9. J. Jurka, V. V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany, and J. Walichiewicz, “Repbase Update, a database of eukaryotic repetitive elements,” Cytogenetic and Genome Research, vol. 110, no. 1–4, pp. 462–467, 2005. View at Publisher · View at Google Scholar
  10. T. Hubbard, D. Andrews, M. Caccamo et al., “Ensembl 2005,” Nucleic Acids Research, vol. 33, supplement 1, pp. D447–D453, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. J. C. Wootton and S. Federhen, “Analysis of compositionally biased regions in sequence databases,” Methods in Enzymology, vol. 266, pp. 554–571, 1996. View at Google Scholar · View at Scopus
  12. W. R. Pearson and D. J. Lipman, “Improved tools for biological sequence comparison,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 8, pp. 2444–2448, 1988. View at Google Scholar · View at Scopus
  13. W. R. Pearson, T. Wood, Z. Zhang, and W. Miller, “Comparison of DNA sequences with protein sequences,” Genomics, vol. 46, no. 1, pp. 24–36, 1997. View at Publisher · View at Google Scholar · View at Scopus
  14. G. Pertea, X. Huang, F. Liang et al., “TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets,” Bioinformatics, vol. 19, no. 5, pp. 651–652, 2003. View at Publisher · View at Google Scholar · View at Scopus
  15. Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, “A greedy algorithm for aligning DNA sequences,” Journal of Computational Biology, vol. 7, no. 1-2, pp. 203–214, 2000. View at Publisher · View at Google Scholar · View at Scopus
  16. X. Huang and A. Madan, “CAP3: a DNA sequence assembly program,” Genome Research, vol. 9, no. 9, pp. 868–877, 1999. View at Publisher · View at Google Scholar · View at Scopus
  17. A. Venktatraman, Validation of a novel EST clustering method and development of a phylogenetic annotation pipeline for livestock gene families, Ph.D. dissertation, Texas A&M University, College Station, Tex, USA, 2008.
  18. G. S. C. Slater and E. Birney, “Automated generation of heuristics for biological sequence comparison,” BMC Bioinformatics, vol. 6, no. 1, article 31, 2005. View at Publisher · View at Google Scholar · View at Scopus
  19. K. Katoh, K. Misawa, K. I. Kuma, and T. Miyata, “MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform,” Nucleic Acids Research, vol. 30, no. 14, pp. 3059–3066, 2002. View at Google Scholar · View at Scopus
  20. J. Felsenstein, PHYLIP (Phylogeny Inference Package) Version 3.6. Distributed by the Author, Department of Genome Sciences, University of Washington, Seattle, Wash, USA, 2005.
  21. W. M. Fitch and E. Margoliash, “Construction of phylogenetic trees,” Science, vol. 155, no. 760, pp. 279–284, 1967. View at Google Scholar · View at Scopus
  22. C. M. Zmasek and S. R. Eddy, “RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs,” BMC Bioinformatics, vol. 3, no. 1, article 14, 2002. View at Google Scholar · View at Scopus
  23. Y. Kapustin, A. Souvorov, T. Tatusova, and D. Lipman, “Splign: algorithms for computing spliced alignments with identification of paralogs,” Biology Direct, vol. 3, article 20, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. R. D. Finn, J. Mistry, J. Tate et al., “The Pfam protein families database,” Nucleic Acids Research, vol. 38, no. 1, pp. D211–D222, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. M. Ashburner, C. A. Ball, J. A. Blake et al., “Gene ontology: tool for the unification of biology,” Nature Genetics, vol. 25, no. 1, pp. 25–29, 2000. View at Publisher · View at Google Scholar · View at Scopus
  26. A. V. Zimin, A. L. Delcher, L. Florea et al., “A whole-genome assembly of the domestic cow, Bos taurus,” Genome Biology, vol. 10, no. 4, article R42, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. T. D. Wu and C. K. Watanabe, “GMAP: a genomic mapping and alignment program for mRNA and EST sequences,” Bioinformatics, vol. 21, no. 9, pp. 1859–1875, 2005. View at Publisher · View at Google Scholar · View at Scopus
  28. D. W. Galbraith, R. Elumalai, and F. C. Gong, “Integrative flow cytometric and microarray approaches for use in transcriptional profiling,” in Flow Cytometry Protocols, vol. 263, pp. 259–279, Humana Press, Totowa, NJ, USA, 2004. View at Google Scholar
  29. G. K. Smyth, Y. H. Yang, and T. Speed, “Statistical issues in cDNA microarray data analysis,” Methods in Molecular Biology, vol. 224, no. 4, pp. 111–136, 2003. View at Google Scholar
  30. “r. R: A language and environment for statistical computing,” R Foundation for Statistical Computing, Vienna, Austria, 2005, http://www.r-project.org/.
  31. A. Kasprzk, D. Keefe, D. Smedley et al., “EnsMart: a generic system for fast and flexible access to biological data,” Genome Research, vol. 14, no. 1, pp. 160–169, 2004. View at Publisher · View at Google Scholar · View at Scopus
  32. M. Lee, C. C. Xiang, J. M. Trent, and M. L. Bittner, “Performance characteristics of 65-mer oligonucleotide microarrays,” Analytical Biochemistry, vol. 368, no. 1, pp. 70–78, 2007. View at Publisher · View at Google Scholar · View at Scopus
  33. H. B. Nielsen, R. Wernersson, and S. Knudsen, “Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays,” Nucleic Acids Research, vol. 31, no. 13, pp. 3491–3496, 2003. View at Publisher · View at Google Scholar · View at Scopus
  34. C. V. Jongeneel, M. Delorenzi, C. Iseli et al., “An atlas of human gene expression from massively parallel signature sequencing (MPSS),” Genome Research, vol. 15, no. 7, pp. 1007–1014, 2005. View at Publisher · View at Google Scholar · View at Scopus
  35. L. L. Hsiao, F. Dangond, T. Yoshida et al., “A compendium of gene expression in normal human tissues,” Physiol Genomics, vol. 7, no. 2, pp. 97–104, 2001. View at Google Scholar · View at Scopus