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TRANSIT - A Software Tool for Himar1 TnSeq Analysis
Open accessAbstract
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.
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A tutorial on hidden Markov models and selected applications in speech recognition
Rabiner, L. R. (1989) · Proceedings of the IEEE · doi:10.1109/5.18626 · Cited by 22,743
Genes required for mycobacterial growth defined by high density mutagenesis
Sassetti, C. M., Boyd, D. H., & Rubin, E. J. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03425.x · Cited by 2,544
Self-citationGriffin, J. E., Gawronski, J. D., DeJesus, M. A., Ioerger, T. R., Akerley, B. J., & Sassetti, C. M. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002251 · Cited by 1,048
Self-citationComparative genomics, minimal gene-sets and the last universal common ancestor
Koonin, E. V. (2003) · Nature Reviews Microbiology · doi:10.1038/nrmicro751 · Cited by 661
Cited by
DeJesus, M. A., Gerrick, E. R., Xu, W., Park, S. W., Long, J. E., Boutte, C. C., Rubin, E. J., Schnappinger, D., Ehrt, S., Fortune, S. M., et al. (2017) · mBio · doi:10.1128/mbio.02133-16 · Cited by 668
Self-citationA decade of advances in transposon-insertion sequencing
Cain, A. K., Barquist, L., Goodman, A. L., Paulsen, I. T., Parkhill, J., & van Opijnen, T. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0244-x · Cited by 391
Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape
Baranowski, C., Welsh, M. A., Sham, L.-T., Eskandarian, H. A., Lim, H. C., Kieser, K. J., Wagner, J. C., McKinney, J. D., Fantner, G. E., Ioerger, T. R., et al. (2018) · eLife · doi:10.7554/elife.37516 · Cited by 132
Self-citationXu, W., DeJesus, M. A., Rücker, N., Engelhart, C. A., Wright, M. G., Healy, C., Lin, K., Wang, R., Park, S. W., Ioerger, T. R., et al. (2017) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01334-17 · Cited by 115
Self-citationWang, Y., Gallagher, L. A., Andrade, P. A., Liu, A., Humphreys, I. R., Turkarslan, S., Cutler, K. J., Arrieta-Ortiz, M. L., Li, Y., Radey, M. C., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.017 · Cited by 108
Metadata
- Authors
- DeJesus, M. A., Ambadipudi, C., Baker, R., Sassetti, C., & Ioerger, T. R.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-10-08
- Volume
- 11
- Issue
- 10
- Pages
- e1004401
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2122385388
- Cited by
- 254
- References
- 4
- FWCI
- 5.14
- Type
- journal article
- Language
- en
- Open access
- gold
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