title: TRANSIT--A Software Tool for Himar1 TnSeq Analysis.
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.
authors.affiliation: Department of Computer Science, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Michael A
authors.initials: MA
authors.lastname: DeJesus
authors.affiliation: Department of Computer Science, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Chaitra
authors.initials: C
authors.lastname: Ambadipudi
authors.affiliation: Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Baker
authors.affiliation: Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
authors.forename: Christopher
authors.initials: C
authors.lastname: Sassetti
authors.affiliation: Department of Computer Science, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Ioerger
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004251:DNA Transposable Elements