References
Borodovsky M, Mills R, Besemer J, Lomsadze A. Prokaryotic gene prediction using GeneMark and GeneMark.hmm. Curr Protoc Bioinforma. 2003. Chapter 4: Unit 4 5.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013;41(Database issue):D226–32.
Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, et al. Genomics. Genome project standards in a new era of sequencing. Science. 2009;326(5950):236–7.
Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, et al. The comprehensive microbial resource. Nucleic Acids Res. 2010;38(Database issue):D340–5.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999;27(23):4636–41.
Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, et al. The “most wanted” taxa from the human microbiome for whole genome sequencing. PLoS ONE. 2012;7(7):e41294.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100–8.
Lasken RS. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol. 2012;10(9):631–40.
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64.
Methé BA, Nelson K, Pop M, Creasy H, Giglio M, Huttenhower C, et al. A framework for human microbiome research. Nature. 2012;486(7402):215–21.
Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328(5981):994–9.
NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. The NIH human microbiome project. Genome Res. 2009;19(12):2317–23.
Proctor LM. The human microbiome project in 2011 and beyond. Cell Host Microbe. 2011;10(4):287–91.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R. et al. InterProScan: protein domains identifier. Nucleic Acids Res 33(Web Server issue): W116–120. 2005.
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;26(13):1608–15.
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Highlander, S. (2014). Human Microbiome Project, Reference Genomes, Rationale, Selection, Acquisition, Sequencing, and Annotation. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_30-1
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DOI: https://doi.org/10.1007/978-1-4614-6418-1_30-1
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