Current Genomics

Christian Néri
Institute of Biology Paris-Seine
CNRS UMR 8256 and UPMC
Paris, 75005
France

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Recognition of Protein-coding Genes Based on Z-curve Algorithms

Author(s): Feng-Biao Guo, Yan Lin and Ling-Ling Chen

Affiliation: College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.

Keywords: Genome annotation, Genome re-annotation, Z-curve algorithm, ZCURVE, ZCURVE_V.

Abstract:

Recognition of protein-coding genes, a classical bioinformatics issue, is an absolutely needed step for annotating newly sequenced genomes. The Z-curve algorithm, as one of the most effective methods on this issue, has been successfully applied in annotating or re-annotating many genomes, including those of bacteria, archaea and viruses. Two Zcurve based ab initio gene-finding programs have been developed: ZCURVE (for bacteria and archaea) and ZCURVE_V (for viruses and phages). ZCURVE_C (for 57 bacteria) and Zfisher (for any bacterium) are web servers for re-annotation of bacterial and archaeal genomes. The above four tools can be used for genome annotation or re-annotation, either independently or combined with the other gene-finding programs. In addition to recognizing protein-coding genes and exons, Z-curve algorithms are also effective in recognizing promoters and translation start sites. Here, we summarize the applications of Z-curve algorithms in gene finding and genome annotation.

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Article Details

VOLUME: 15
ISSUE: 2
Page: [95 - 103]
Pages: 9
DOI: 10.2174/1389202915999140328162724