Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries

Sina Solaimanpour; Felipe Sarmiento; Jan Mrázek

doi:10.1371/journal.pone.0126070

Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries

PLoS One. 2015 May 4;10(5):e0126070. doi: 10.1371/journal.pone.0126070. eCollection 2015.

Authors

Sina Solaimanpour¹, Felipe Sarmiento², Jan Mrázek³

Affiliations

¹ Department of Computer Science, University of Georgia, Athens, GA 30602, United States of America.
² Swissaustral USA, 111 Riverbend Rd., Athens, GA 30602, United States of America.
³ Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, United States of America.

Abstract

Tn-seq is a high throughput technique for analysis of transposon mutant libraries. Tn-seq Explorer was developed as a convenient and easy-to-use package of tools for exploration of the Tn-seq data. In a typical application, the user will have obtained a collection of sequence reads adjacent to transposon insertions in a reference genome. The reads are first aligned to the reference genome using one of the tools available for this task. Tn-seq Explorer reads the alignment and the gene annotation, and provides the user with a set of tools to investigate the data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. Emphasis is placed on providing flexibility in selecting parameters and methodology most appropriate for each particular dataset. Tn-seq Explorer is written in Java as a menu-driven, stand-alone application. It was tested on Windows, Mac OS, and Linux operating systems. The source code is distributed under the terms of GNU General Public License. The program and the source code are available for download at http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/ and https://github.com/sina-cb/Tn-seqExplorer.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bacteria / genetics
Computational Biology / methods*
DNA Transposable Elements
Databases, Nucleic Acid
Gene Library
Genomics / methods*
High-Throughput Nucleotide Sequencing
Mutation
Software*

Substances

DNA Transposable Elements

Grants and funding

This work was supported by the National Science Foundation grant number DBI-0950266. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Swissaustral USA provided support in the form of salaries for author FS, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.