TRANSIT--A Software Tool for Himar1 TnSeq Analysis

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. TRA...

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Bibliographic Details
Published in:PLoS computational biology 2015-10, Vol.11 (10), p.e1004401-e1004401
Main Authors: DeJesus, Michael A, Ambadipudi, Chaitra, Baker, Richard, Sassetti, Christopher, Ioerger, Thomas R
Format: Article
Language:English
Subjects:
Algorithms
Analysis
Bacterial genetics
Base Sequence
Binomial distribution
Cholesterol
Chromosome Mapping - methods
Comparative analysis
Datasets
DNA Transposable Elements - genetics
Equipment and supplies
Experiments
Funding
Genome, Bacterial - genetics
Genomes
Glycerol
Influenza
Linux
Methods
Modems
Molecular Sequence Data
Pattern Recognition, Automated - methods
Programming Languages
Sequence Analysis, DNA - methods
Software
Tuberculosis
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Summary: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.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1004401