title: ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes.
abstract: In 2003, we developed an ab initio program, ZCURVE 1.0, to find genes in bacterial and archaeal genomes. In this work, we present the updated version (i.e. ZCURVE 3.0). Using 422 prokaryotic genomes, the average accuracy was 93.7% with the updated version, compared with 88.7% with the original version. Such results also demonstrate that ZCURVE 3.0 is comparable with Glimmer 3.02 and may provide complementary predictions to it. In fact, the joint application of the two programs generated better results by correctly finding more annotated genes while also containing fewer false-positive predictions. As the exclusive function, ZCURVE 3.0 contains one post-processing program that can identify essential genes with high accuracy (generally >90%). We hope ZCURVE 3.0 will receive wide use with the web-based running mode. The updated ZCURVE can be freely accessed from http://cefg.uestc.edu.cn/zcurve/ or http://tubic.tju.edu.cn/zcurveb/ without any restrictions.
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Zhi-Gang
authors.initials: ZG
authors.lastname: Hua
authors.affiliation: Department of Physics, Tianjin University, Tianjin 300072, China Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Ya-Zhou
authors.initials: YZ
authors.lastname: Yuan
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: De-Chang
authors.initials: DC
authors.lastname: Yang
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wei
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China fbguo@uestc.edu.cn.
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
mesh_terms: D000465:Algorithms; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020043:Genes, Essential; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D020407:Internet; D012984:Software