IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1004401.html
   My bibliography  Save this article

TRANSIT - A Software Tool for Himar1 TnSeq Analysis

Author

Listed:
  • Michael A DeJesus
  • Chaitra Ambadipudi
  • Richard Baker
  • Christopher Sassetti
  • Thomas R Ioerger

Abstract

TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit

Suggested Citation

  • Michael A DeJesus & Chaitra Ambadipudi & Richard Baker & Christopher Sassetti & Thomas R Ioerger, 2015. "TRANSIT - A Software Tool for Himar1 TnSeq Analysis," PLOS Computational Biology, Public Library of Science, vol. 11(10), pages 1-17, October.
    • Handle: RePEc:plo:pcbi00:1004401
    DOI: 10.1371/journal.pcbi.1004401
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004401
    Download Restriction: no
    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004401&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pcbi.1004401?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. Aldert Zomer & Peter Burghout & Hester J Bootsma & Peter W M Hermans & Sacha A F T van Hijum, 2012. "ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-9, August.
    2. Justin R Pritchard & Michael C Chao & Sören Abel & Brigid M Davis & Catherine Baranowski & Yanjia J Zhang & Eric J Rubin & Matthew K Waldor, 2014. "ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing," PLOS Genetics, Public Library of Science, vol. 10(11), pages 1-15, November.
    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. Samuel Miravet-Verde & Rocco Mazzolini & Carolina Segura-Morales & Alicia Broto & Maria Lluch-Senar & Luis Serrano, 2024. "ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Henri Voedts & Sean P. Kennedy & Guennadi Sezonov & Michel Arthur & Jean-Emmanuel Hugonnet, 2022. "Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli revealed unexpected impacts of β-lactams," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Di Qu & Peng Ge & Laure Botella & Sae Woong Park & Ha-Na Lee & Natalie Thornton & James M. Bean & Inna V. Krieger & James C. Sacchettini & Sabine Ehrt & Courtney C. Aldrich & Dirk Schnappinger, 2024. "Mycobacterial biotin synthases require an auxiliary protein to convert dethiobiotin into biotin," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    4. Kaj M. Kreutzfeldt & Robert S. Jansen & Travis E. Hartman & Alexandre Gouzy & Ruojun Wang & Inna V. Krieger & Matthew D. Zimmerman & Martin Gengenbacher & Jansy P. Sarathy & Min Xie & Véronique Dartoi, 2022. "CinA mediates multidrug tolerance in Mycobacterium tuberculosis," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Jeffrey A. Freiberg & Valeria M. Reyes Ruiz & Brittney D. Gimza & Caitlin C. Murdoch & Erin R. Green & Jacob M. Curry & James E. Cassat & Eric P. Skaar, 2024. "Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

    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. Hong Yang & Elias W Krumholz & Evan D Brutinel & Nagendra P Palani & Michael J Sadowsky & Andrew M Odlyzko & Jeffrey A Gralnick & Igor G L Libourel, 2014. "Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis," PLOS Computational Biology, Public Library of Science, vol. 10(9), pages 1-10, September.

    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:pcbi00:1004401. 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: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    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.