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Naming and Annotation of Plasmids

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Molecular Life Sciences

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References

  1. Klimke W, O’Donovan C, White O et al (2011) Solving the problem: genome annotation standards before the data deluge. Stand Genomic Sci 5(1):168–193

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. Brister JR, Bao Y, Kuiken C et al (2010) Towards viral genome annotation standards, report from the 2010 NCBI annotation workshop. Viruses 2(10):2258–2268

    Article  PubMed Central  PubMed  Google Scholar 

  3. Sen D, Van der Auwera GA, Rogers LM et al (2011) Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol 77(22):7975–7983

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Novick RP, Clowes RC, Cohen SN et al (1976) Uniform nomenclature for bacterial plasmids: a proposal. Bacteriol Rev 40(1):168–189

    CAS  PubMed Central  PubMed  Google Scholar 

  5. Achtman M, Willetts NS, Clark AJ (1971) Beginning a genetic analysis of conjugational transfer determined by the F factor in Escherichia coli by isolation and characterization of transfer-deficient mutants. J Bacteriol 106(2):529–538

    CAS  PubMed Central  PubMed  Google Scholar 

  6. Frost LS, Ippen-Ihler K, Skurray RA (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev 58(2):162–210

    CAS  PubMed Central  PubMed  Google Scholar 

  7. Pansegrau W, Lanka E, Barth PT et al (1994) Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis. J Mol Biol 239(5):623–663

    Article  CAS  PubMed  Google Scholar 

  8. Alvarez-Martinez CE, Christie PJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73(4):775–808

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Sciaky D, Montoya AL, Chilton MD (1978) Fingerprints of Agrobacterium Ti plasmids. Plasmid 1(2):238–253

    Article  CAS  PubMed  Google Scholar 

  10. Roberts RJ, Belfort M, Bestor T et al (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31(7):1805–1812

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Demerec M, Adelberg EA, Clark AJ et al (1966) A proposal for a uniform nomenclature in bacterial genetics. Genetics 54(1):61–76

    CAS  PubMed Central  PubMed  Google Scholar 

  12. Siguier P, Varani A, Perochon J et al (2012) Exploring bacterial insertion sequences with ISfinder: objectives, uses, and future developments. Methods Mol Biol 859:91–103

    Article  CAS  PubMed  Google Scholar 

  13. FTP directory of genomes/plasmids. ftp://ftp.ncbi.nih.gov/genomes/Plasmids/. Accessed 16 Mar 2014

  14. International Nucleotide Sequence Database Collaboration (INSDC). http://www.insdc.org/. Accessed 16 Mar 2014

  15. NCBI GenBank home page. http://www.ncbi.nlm.nih.gov/genbank/. Accessed 16 Mar 2014

  16. NCBI GenBank bacterial genome submission guide (annotation). http://www.ncbi.nlm.nih.gov/GenBank/genomesubmit_annotation. Accessed 16 Mar 2014

  17. NCBI GenBank bacterial genome submission guide (locus tag). http://www.ncbi.nlm.nih.gov/genbank/genomesubmit#locus_tag. Accessed 16 Mar 2014

  18. NCBI GenBank metagenome submission guide. http://www.ncbi.nlm.nih.gov/genbank/metagenome. Accessed 16 Mar 2014

  19. NCBI GenBank whole genome shotgun submissions guide. http://www.ncbi.nlm.nih.gov/genbank/wgs. Accessed 16 Mar 2014

  20. NCBI handbook. http://www.ncbi.nlm.nih.gov/books/NBK21105/. Accessed 16 Mar 2014

  21. NCBI reference sequence database. http://www.ncbi.nlm.nih.gov/RefSeq/. Accessed 16 Mar 2014

  22. Swiss-Prot Group http://web.expasy.org/groups/swissprot/. Accessed 16 Mar 2014

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Acknowledgments

The authors wish to thank Celeste Brown (University of Idaho), Bill Klimke (NCBI), and Miguel Cevallos (CFN, Mexico) for useful discussions.

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Correspondence to Laura S. Frost .

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Frost, L.S., Thomas, C.M. (2014). Naming and Annotation of Plasmids. In: Bell, E. (eds) Molecular Life Sciences. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6436-5_568-2

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  • DOI: https://doi.org/10.1007/978-1-4614-6436-5_568-2

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