Avianbase: a community resource for bird genomics
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  • 作者:Lél E?ry ; M Thomas P Gilbert ; Cai Li ; Bo Li ; Alan Archibald
  • 刊名:Genome Biology
  • 出版年:2015
  • 出版时间:December 2015
  • 年:2015
  • 卷:16
  • 期:1
  • 全文大小:1,242 KB
  • 参考文献:1. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346:1320-1. CrossRef
    2. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014;346:1311-0. CrossRef
    3. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al. Phylogenomic analyses data of the Avian Phylogenomics Project. GigaScience. 2014. http://dx.doi.org/10.5524/101041. Accessed 13 January 2015.
    4. Zhang G, Li B, Li C, Gilbert MPT, Jarvis ED, Wang J. Comparative genomic data of the Avian Phylogenomics Project. GigaScience. 2014. doi:10.1186/2047-217×-3-26. Accessed 13 January 2015.
    5. Genome 10?K Community of Scientists. Genome 10?K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009;100:659-4. CrossRef
    6. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic Acids Res. 2014;42(Database issue):D749-5. CrossRef
    7. Kitts P. Genome assembly and annotation process. In: McEntyre J, Ostell J, editors. The NCBI handbook. Bethesda, MD National Center for Biotechnology Information (US); 2002 (updated 2003). http://www.ncbi.nlm.nih.gov/books/NBK21086/. Accessed 11 December 2014.
    8. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42(Database issue), D76470.
    9. Severin J, Beal K, Vilella AJ, Fitzgerald S, Schuster M, Gordon L, et al. eHive: an artificial intelligence workflow system for genomic analysis. BMC Bioinformatics. 2010;11:240. CrossRef
    10. Camacho C, Madden T, Ma N, Tao T, Agarwala A, Morgulis A. BLAST command line applications user manual. In: BLAST? Help. Bethesda, MD: National Center for Biotechnology Information (US); 2008 (updated 2014). http://www.ncbi.nlm.nih.gov/books/NBK1763/. Accessed 11 December 2014.
    11. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-0. CrossRef
    12. Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996-2010. http://www.repeatmasker.org. Accessed 11 December 2014.
    13. Smit AFA, Hubley R. RepeatModeler Open-1.0. 2008-2010. http://www.repeatmasker.org. Accessed 11 December 2014.
    14. Birney E, Clamp M, Durbin R. GeneWise and genomewise. Genome Res. 2004;14:988-5. CrossRef
    15. Phylogenomics analysis of birds. http://phybirds.genomics.org.cn. Accessed 11 December 2014.
    16. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011;478:476-2. CrossRef
    17. Rubin C-J, Zody MC, Eriksson J, Meadows JRS, Sherwood E, Webster MT, et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010;464:587-1. CrossRef
    18. National Avian Research Facility, University of Edinburgh. 2015. http://www.narf.ac.uk/. Accessed 13 January 2015.
  • 作者单位:Lél E?ry (1)
    M Thomas P Gilbert (2) (3)
    Cai Li (2) (4)
    Bo Li (2) (4) (5)
    Alan Archibald (1)
    Bronwen L Aken (6) (7)
    Guojie Zhang (4) (8)
    Erich Jarvis (9)
    Paul Flicek (6) (7)
    David W Burt (1)

    1. Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
    2. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ?ster Voldgade 5-7, 1350, Copenhagen, Denmark
    3. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia
    4. China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
    5. College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, 710061, China
    6. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    7. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    8. Center for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100, Denmark
    9. Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC, 27710, USA
  • 刊物主题:Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
  • 出版者:BioMed Central
  • ISSN:1465-6906
文摘
Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium.

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