ZCURVE 3.0: Identify Prokaryotic Genes With Higher Accuracy as Well as Automatically and Accurately Select Essential Genes

Nucleic Acids Res. 2015 Jul 1;43(W1):W85-90. doi: 10.1093/nar/gkv491. Epub 2015 May 14.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Genes, Archaeal*
  • Genes, Bacterial*
  • Genes, Essential
  • Genome, Archaeal
  • Genome, Bacterial
  • Internet
  • Software*