Bioinformatics. Группа авторов

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Bioinformatics - Группа авторов


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Rat Genome Database rgd.mcw.edu Other genome resources GENCODE www.gencodegenes.org Genome Reference Consortium www.ncbi.nlm.nih.gov/grc GWAS Catalog www.ebi.ac.uk/gwas National Center for Biotechnology Information (NCBI) Genome Data Viewer www.ncbi.nlm.nih.gov/genome/gdv National Institutes of Health (NIH) Genomic Data Sharing Policyies osp.od.nih.gov/scientific-sharing/policies NIH Genotype-Tissue Expression (GTEx) Portal www.gtexportal.org Track Hub Registry www.trackhubregistry.org

      The best way to learn about the data and tools available in the UCSC and Ensembl Genome Browsers is to read the relevant sections of the online documentation that accompanies each browser. The documentation on both sites is extensive and up to date, and will likely answer the user's questions. Alternatively, specialized questions can be addressed by contacting the web site development teams. URLs are listed in the Internet Resources section of this chapter.

      The Database issue of Nucleic Acids Research, published in January of each year, usually includes articles that provide a broad overview of each Genome Browser as well as a description of new data and resources. The references for 2019 are listed below, and additional information can be found in Chapter 1.

      1 Aken, B.L., Ayling, S., Barrell, D. et al. (2016). The Ensembl gene annotation system. Database (Oxford) 2016, pii: baw093.

      2 Benson, D.A., Boguski, M.S., Lipman, D.J., and Ostell, J. (1997). GenBank. Nucleic Acids Res. 25 (1): 1–6.

      3 Buels, R., Yao, E., Diesh, C.M. et al. (2016). JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 17: 66.

      4 Buniello, A., MacArthur, J.A.L., Cerezo, M. et al. (2019). The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics. Nucleic Acids Res. 47 (D1): D1005–D1012.

      5 Camacho, C., Coulouris, G., Avagyan, V. et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10: 421.

      6 Cunningham, F., Achuthan, P., Akanni, W. et al. (2019). Ensembl 2019. Nucleic Acids Res 47 (D1): D745–D751.

      7 ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489 (7414): 57–74.

      8 Frankish, A., Uszczynska, B., Ritchie, G.R. et al. (2015). Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics 16 (Suppl 8): S2.

      9 Goffeau, A., Barrell, B.G., Bussey, H. et al. (1996). Life with 6000 genes. Science 274 (5287): 546, 563–567.

      10 Green, E.D. (2001). Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2 (8): 573–583.

      11 GTEx Consortium (2015). Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348 (6235): 648–660.

      12 Haeussler, M., Zweig, A.S., Tyner, C. et al. (2019). The UCSC Genome Browser database: 2019 update. Nucleic Acids Res 47 (D1): D853–D858.

      13 Harrow, J., Frankish, A., Gonzalez, J.M. et al. (2012). GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22 (9): 1760–1774.

      14 Herrero, J., Muffato, M., Beal, K. et al. (2016). Ensembl comparative genomics resources. Database (Oxford) 2016: bav096.

      15 Howald, C., Tanzer, A., Chrast, J. et al. (2012). Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res. 22 (9): 1698–1710.

      16 Hubbard, T., Barker, D., Birney, E. et al. (2002). The Ensembl genome database project. Nucleic Acids Res. 30 (1): 38–41.

      17 Kent, W.J. (2002). BLAT–the BLAST-like alignment tool. Genome Res. 12 (4): 656–664.

      18 Kent, W.J. and Haussler, D. (2001). Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11 (9): 1541–1548.

      19 Kent, W.J. and Zahler, A.M. (2000). The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Nucleic Acids Res. 28 (1): 91–93.

      20 Kinsella, R.J., Kähäri, A., Haider, S. et al. (2011). Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011: bar030.

      21 Kitts, P. (2003). Genome assembly and annotation process. In: The NCBI Handbook (eds. J. McEntyre and J. Ostell) ch. 14. Bethesda, MD: National Center for Biotechnology Information.

      22 Lander, E.S., Linton, L.M., Birren, B. et al., and International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409 (6822): 860–921.

      23 Lawrence, M., Daujat, S., and Schneider, R. (2016). Lateral thinking: how histone modifications regulate gene expression. Trends Genet. 32 (1): 42–56.

      24 Li, R., Fan, W., Tian, G. et al. (2010). The sequence and de novo assembly of the giant panda genome. Nature 463 (7279): 311–317.

      25 McLaren, W., Gil, L., Hunt, S.E. et al. (2016). The Ensembl variant effect predictor. Genome Biol. 17 (1): 122.

      26 Moreland, R.T., Nguyen, A.D., Ryan, J.F. et al. (2014). A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics 15: 316.

      27 Mudge, J.M. and Harrow, J. (2015). Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm. Genome 26 (9–10): 366–378.

      28 Ryan, J.F., Pang, K., Schnitzler, C.E. et al. (2013). The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342 (6164): 1242592.

      29 Sayers, E.W., Agarwala, R., Bolton, E.E. et al. (2019). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 47 (D1): D23–D28.

      30 Skinner, M.E. and Holmes, I.H. (2010). Setting up the JBrowse genome browser. Curr. Protoc. Bioinformatics. Chapter 9: Unit 9.13. https://doi.org/10.1002/0471250953.bi0913s32.

      31 Trapnell, C., Williams, B.A., Pertea, G. et al. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28 (5): 511–515.

      32 Wheeler, D.L., Church, D.M., Lash, A.E. et al. (2001). Database resources of the National


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