Skip to main content
SpringerLink
Log in
Book cover

Horizontal Gene Transfer pp 341–353Cite as

Statistical Analysis of Accessory Genome

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2075))

Abstract

AcCNET (Accessory genome Constellation Network) is a Perl application to determine the variation of content in any genomic unit (e.g., bacterial genomes, plasmids, and transposons) within large datasets. It provides functional information that can be handled and visualized interactively as a bipartite network. In this chapter, we explain how to perform a statistical analysis of AcCNET data.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8(9):396–401

    Article  CAS  PubMed  Google Scholar 

  2. Rosselló-Móra R, Amann R (2015) Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 38:209–216. https://doi.org/10.1016/j.syapm.2015.02.001

    Article  PubMed  Google Scholar 

  3. Vernikos G, Medini D, Riley DR, Tettelin H (2015) Ten years of pan-genome analyses. Curr Opin Microbiol 23:148–154. https://doi.org/10.1016/j.mib.2014.11.016

    Article  CAS  PubMed  Google Scholar 

  4. Lanza VF, Baquero F, de la Cruz F, Coque TM (2017) AcCNET (accessory genome constellation network): comparative genomics software for accessory genome analysis using bipartite networks. Bioinformatics 33:283–285. https://doi.org/10.1093/bioinformatics/btw601

    Article  CAS  PubMed  Google Scholar 

  5. R Development Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. R Found. Stat. Comput. Vienna, Austria

    Google Scholar 

  6. RStudio Team (2015) RStudio: integrated development for R. [online]. RStudio, Inc, Boston, MA. http//www rstudio com. https://doi.org/10.1126/science.aad6351

    Book  Google Scholar 

  7. Bastian M, Heymann S, Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. Third Int AAAI Conf Weblogs Soc Media:361–362. https://doi.org/10.1136/qshc.2004.010033

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Microbiology, Ramón y Cajal Universitary Hospital (IRYCIS), Madrid, Spain

    Miguel D. Fernández-de-Bobadilla

  2. Department of Microbiology, Ramón y Cajal Research Institute (IRYCIS), Madrid, Spain

    Teresa M. Coque

  3. CIBER in Epidemiology and Public Health, (CIBERESP), Madrid, Spain

    Teresa M. Coque

  4. Bioinformatics Unit, Ramón y Cajal Universitary Hospital (IRYCIS), Madrid, Spain

    Val F. Lanza

Authors
  1. Miguel D. Fernández-de-Bobadilla
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Teresa M. Coque
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Val F. Lanza
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Cantabria, Spain

    Fernando de la Cruz

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Fernández-de-Bobadilla, M.D., Coque, T.M., Lanza, V.F. (2020). Statistical Analysis of Accessory Genome. In: de la Cruz, F. (eds) Horizontal Gene Transfer. Methods in Molecular Biology, vol 2075. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9877-7_24

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9877-7_24

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9876-0

  • Online ISBN: 978-1-4939-9877-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation