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Front Microbiol. 2017 Nov 27;8:2331. doi: 10.3389/fmicb.2017.02331. eCollection 2017.

A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes.

Peng C1, Lin Y1, Luo H1, Gao F1,2,3.

Author information

1
Department of Physics, School of Science, Tianjin University, Tianjin, China.
2
Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.
3
SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China.

Abstract

Genes critical for the survival or reproduction of an organism in certain circumstances are classified as essential genes. Essential genes play a significant role in deciphering the survival mechanism of life. They may be greatly applied to pharmaceutics and synthetic biology. The continuous progress of experimental method for essential gene identification has accelerated the accumulation of gene essentiality data which facilitates the study of essential genes in silico. In this article, we present some available online resources related to gene essentiality, including bioinformatic software tools for transposon sequencing (Tn-seq) analysis, essential gene databases and online services to predict bacterial essential genes. We review several computational approaches that have been used to predict essential genes, and summarize the features used for gene essentiality prediction. In addition, we evaluate the available online bacterial essential gene prediction servers based on the experimentally validated essential gene sets of 30 bacteria from DEG. This article is intended to be a quick reference guide for the microbiologists interested in the essential genes.

KEYWORDS:

Tn-seq analysis; essential gene; gene essentiality prediction; minimal gene set; synthetic biology

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