IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0221631.html
   My bibliography  Save this article

Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction

Author

Listed:
  • Daniel Gamermann
  • Arnau Montagud
  • J Alberto Conejero
  • Pedro Fernández de Córdoba
  • Javier F Urchueguía

Abstract

Dendrograms are a way to represent relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic material of choice for the sequence alignments (all the genes or sets of genes) results in distinct inferred dendrograms. In this work, we evaluate differences between dendrograms reconstructed with different methodologies and for different sets of organisms chosen at random from a much larger set. A statistical analysis is performed to estimate fluctuations between the results obtained from the different methodologies that allows us to validate a systematic approach, based on the comparison of the organisms’ metabolic networks for inferring dendrograms. This has the advantage that it allows the comparison of organisms very far away in the evolutionary tree even if they have no known ortholog gene in common. Our results show that dendrograms built using information from metabolic networks are similar to the standard sequence-based dendrograms and can be a complement to them.

Suggested Citation

  • Daniel Gamermann & Arnau Montagud & J Alberto Conejero & Pedro Fernández de Córdoba & Javier F Urchueguía, 2019. "Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction," PLOS ONE, Public Library of Science, vol. 14(9), pages 1-13, September.
    • Handle: RePEc:plo:pone00:0221631
    DOI: 10.1371/journal.pone.0221631
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221631
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0221631&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0221631?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Anonymous, 2013. "Notes from the Editors," American Political Science Review, Cambridge University Press, vol. 107(4), pages 1-1, November.
    2. Anonymous, 2013. "Notes from the Editors," American Political Science Review, Cambridge University Press, vol. 107(3), pages 1-1, August.
    3. Anonymous, 2013. "Notes from the Editors," American Political Science Review, Cambridge University Press, vol. 107(2), pages 1-1, May.
    4. Anonymous, 2013. "Notes from the Editors," American Political Science Review, Cambridge University Press, vol. 107(1), pages 1-1, February.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Gamermann, Daniel & Pellizzaro, José Antônio, 2022. "An algorithm for network community structure determination by surprise," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 595(C).

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Naomi Prachi Hazarika, 2020. "Spaces of Intermediation and Political Participation: a Study of KuSumpur pahadI redevelopment project," CSH-IFP Working Papers 0016, Centre de Sciences Humaines, New Delhi, revised Jul 2020.
    2. Mohammad Amini Farsani & Esmat Babaii, 2020. "Applied linguistics research in three decades: a methodological synthesis of graduate theses in an EFL context," Quality & Quantity: International Journal of Methodology, Springer, vol. 54(4), pages 1257-1283, August.
    3. Fabio Gobbi, 2021. "Evaluating Forecasts from State-Dependent Autoregressive Models for US GDP Growth Rate. Comparison with Alternative Approaches," Advances in Management and Applied Economics, SCIENPRESS Ltd, vol. 11(6), pages 1-7.
    4. S M Ferdous & M Sohel Rahman, 2015. "An Integer Programming Formulation of the Minimum Common String Partition Problem," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-16, July.
    5. Jin Qi & Zhiyong Yang, 2014. "Learning Dictionaries of Sparse Codes of 3D Movements of Body Joints for Real-Time Human Activity Understanding," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-24, December.
    6. Kwangsu Lee & Dong Hoon Lee, 2015. "Security Analysis of the Unrestricted Identity-Based Aggregate Signature Scheme," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-8, May.
    7. A F M Saifuddin Saif & Anton Satria Prabuwono & Zainal Rasyid Mahayuddin, 2015. "Moment Feature Based Fast Feature Extraction Algorithm for Moving Object Detection Using Aerial Images," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-11, June.
    8. Mohammad Amini Farsani & Esmat Babaii & Maryam Beikmohammadi & Meysam Babaii Farsani, 2022. "Mixed-methods research proficiency for applied linguists: a PLS-path modelling approach," Quality & Quantity: International Journal of Methodology, Springer, vol. 56(5), pages 3337-3362, October.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0221631. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.