• Login
View Item 
  • DASH Home
  • Faculty of Arts and Sciences
  • FAS Scholarly Articles
  • View Item
  • DASH Home
  • Faculty of Arts and Sciences
  • FAS Scholarly Articles
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

Browse

All of DASH
  • Communities & Collections
  • By Issue Date
  • Author
  • Title
  • Keyword
  • FAS Department
This Collection
  • By Issue Date
  • Author
  • Title
  • Keyword
  • FAS Department

Submitters

  • Login
  • Quick submit
  • Waiver Generator

About

  • About DASH
  • DASH Stories
  • DASH FAQs
  • Accessibility
  • COVID-related Research
  • Terms of Use
  • Privacy Policy

Statistics

  • By Schools
  • By Collections
  • By Departments
  • By Items
  • By Country
  • By Authors

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data

 
Thumbnail
View/Open
3799429.pdf (9.330Mb)
Author
Chao, Michael C.HARVARD
Pritchard, Justin R.
Zhang, Yanjia J.HARVARD
Rubin, Eric J.HARVARD
Livny, JonathanHARVARD
Davis, Brigid M.HARVARD
Waldor, Matthew K.HARVARD
Published Version
https://doi.org/10.1093/nar/gkt654
Metadata
Show full item record
Citation
Chao, Michael C., Justin R. Pritchard, Yanjia J. Zhang, Eric J. Rubin, Jonathan Livny, Brigid M. Davis, and Matthew K. Waldor. 2013. “High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data.” Nucleic Acids Research 41 (19): 9033-9048. doi:10.1093/nar/gkt654. http://dx.doi.org/10.1093/nar/gkt654.
Abstract
The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data.
Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799429/pdf/
Terms of Use
This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page
http://nrs.harvard.edu/urn-3:HUL.InstRepos:11878850

Collections
  • FAS Scholarly Articles [18179]
  • HMS Scholarly Articles [17878]
  • SPH Scholarly Articles [6354]

Contact administrator regarding this item (to report mistakes or request changes)

e: osc@harvard.edu

t: +1 (617) 495 4089

Creative Commons license‌Creative Commons Attribution 4.0 International License

Except where otherwise noted, this work is subject to a Creative Commons Attribution 4.0 International License, which allows anyone to share and adapt our material as long as proper attribution is given. For details and exceptions, see the Harvard Library Copyright Policy ©2022 Presidents and Fellows of Harvard College.

  • Follow us on Twitter
  • Contact
  • Harvard Library
  • Harvard University