Bovine Genome Database: Integrated tools for genome annotation and discovery

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Childers, Christopher P ^a   Reese, Justin T ^b   Sundaram, Jaideep P ^a   Vile, Donald C ^a   Dickens, C Michael ^b   Childs, Kevin L ^b,c   Salih, Hanni ^b   Bennett, Anna K ^a   Hagen, Darren E ^a   Adelson, David L ^b,d   Elsik, Christine G ^b  

^a GEORGETOWN UNIVERSITY   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; UNTRANSLATED RNA;

ACCESS TO INFORMATION; ARTICLE; COMPUTER INTERFACE; COW; EXPRESSED SEQUENCE TAG; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC DATABASE; GENOME ANALYSIS; GENOMICS; NONHUMAN; PRIORITY JOURNAL; PSEUDOGENE; QUANTITATIVE TRAIT LOCUS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATTLE; DATABASES, GENETIC; GENOME; GENOMICS; MODELS, GENETIC; MOLECULAR SEQUENCE ANNOTATION; QUANTITATIVE TRAIT LOCI; SEQUENCE ALIGNMENT; SOFTWARE; SYSTEMS INTEGRATION;

BOVINAE;

EID: 78651321210     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1235     Document Type: Article

References (29)

1. Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P., Da, Y., VanRaden, P.M., Ron, M., Weller, J.I. and Lewin, H.A. (2004) Detection of quantitative trait loci affecting milk production, health, and reproductive traits in holstein cattle. J. Dairy Sci., 87, 468-475.
2. Keele, J.W., Shackelford, S.D., Kappes, S.M., Koohmaraie, M. and Stone, R.T. (1999) A region on bovine chromosome 15 influences beef tenderness in steers. J. Anim. Sci., 77, 1364-1371.
3. Mallard, B.A., Dekkers, J.C., Ireland, M.J., Leslie, K.E., Sharif, S., Vankampen, C.L., Wagter, L. and Wilkie, B.N. (1998) Alteration in immune responsiveness during the peripartum period and its ramification on dairy cow and calf health. J. Dairy Sci., 81, 585-595.
4. Park, Y.H., Joo, Y.S., Park, J.Y., Moon, J.S., Kim, S.H., Kwon, N.H., Ahn, J.S., Davis, W.C. and Davies, C.J. (2004) Characterization of lymphocyte subpopulations and major histocompatibility complex haplotypes of mastitis-resistant and susceptible cows. J. Vet. Sci., 5, 29-39.
5. Bovine Genome Sequencing and Analysis Consortium. (2009) The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science, 324, 522-528.
6. Liu, Y., Qin, X., Song, X.Z., Jiang, H., Shen, Y., Durbin, K.J., Lien, S., Kent, M.P., Sodeland, M., Ren, Y. et al. (2009) Bos taurus genome assembly. BMC Genomics, 10, 180.
7. Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T. and Birney, E. (2004) EnsMart: A generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
8. Lewis, S.E., Searle, S.M., Harris, N., Gibson, M., Lyer, V., Richter, J., Wiel, C., Bayraktaroglir, L., Birney, E., Crosby, M.A. et al. (2002) Apollo: A sequence annotation editor. Genome Biol., 3, RESEARCH0082.
9. Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R. et al. (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res., 37, D555-D559.
10. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
11. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
12. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Federhen, S. et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 38, D5-D16.
13. Flicek, P., Aken, B.L., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S. et al. (2010) Ensembl's 10th year. Nucleic Acids Res., 38, D557-D562.
14. Rhead, B., Karolchik, D., Kuhn, R.M., Hinrichs, A.S., Zweig, A.S., Fujita, P.A., Diekhans, M., Smith, K.E., Rosenbloom, K.R., Raney, B.J. et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res., 38, D613-D619.
15. Pruitt, K.D., Tatusova, T., Klimke, W. and Maglott, D.R. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res., 37, D32-D36.
16. Curwen, V., Eyras, E., Andrews, T.D., Clarke, L., Mongin, E., Searle, S.M. and Clamp, M. (2004) The Ensembl automatic gene annotation system. Genome Res., 14, 942-950.
17. Salamov, A.A. and Solovyev, V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res., 10, 516-522.
18. Solovyev, V. (2007) In Balding, D.J., Bishop, M. and Cannings, C. (eds), Handbook of Statistical Genetics. John Wiley & Sons, Chichester, UK, Hoboken, NJ, pp. 97-159.
19. Blanco, E., Parra, G. and Guigo, R. (2007) Using geneid to identify genes. Curr. Protoc. Bioinformatics, Chapter 4, Unit 4 3.
20. Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W. and Guigo, R. (2003) Comparative gene prediction in human and mouse. Genome Res., 13, 108-117.
21. Wu, T.D. and Watanabe, C.K. (2005) GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875.
22. Slater, G.S. and Birney, E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
23. Polineni, P., Aragonda, P., Xavier, S.R., Furuta, R. and Adelson, D.L. (2006) The bovine QTL viewer: A web accessible database of bovine Quantitative Trait Loci. BMC Bioinformatics, 7, 283.
24. Salih, H. and Adelson, D.L. (2009) QTL global meta-analysis: Are trait determining genes clustered? BMC Genomics, 10, 184.
25. Elsik, C.G., Mackey, A.J., Reese, J.T., Milshina, N.V., Roos, D.S. and Weinstock, G.M. (2007) Creating a honey bee consensus gene set. Genome Biol., 8, R13.
26. Reese, J.T., Childers, C.P., Sundaram, J.P., Vile, D.C., Dickens, C.M., Childs, K.L. and Elsik, C.G. (2010) Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome. BMC Genomics, 11, 645.
27. Carbon, S., Ireland, A., Mungall, C.J., Shu, S., Marshall, B. and Lewis, S. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics, 25, 288-289.
28. Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S. et al. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol, 10, R42.
29. Haider, S., Ballester, B., Smedley, D., Zhang, J., Rice, P. and Kasprzyk, A. (2009) BioMart Central Portal-unified access to biological data. Nucleic Acids Res., 37(Web Server issue), W23-W27.