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PEP_scaffolder: using (homologous) proteins to scaffold genomes

文献类型： 外文期刊

作者： Zhu, Bai-Han 1 ; Song, Ying-Nan 1 ; Xue, Wei 2 ; Xu, Gui-Cai 2 ; Xiao, Jun 1 ; Sun, Ming-Yuan 1 ; Sun, Xiao-Wen 2 ; Li, J 1 ;

作者机构： 1.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China

2.Chinese Acad Fishery Sci, Ctr Appl Aquat Genom, Beijing 100141, Peoples R China

3.Zhejiang Ocean Univ, Coll Marine Sci, Zhoushan 316022, Peoples R China

期刊名称：BIOINFORMATICS （ 影响因子：6.937； 五年影响因子：8.47 ）

ISSN： 1367-4803

年卷期： 2016 年 32 卷 20 期

页码：

收录情况： SCI

摘要： Motivation: Recovering the gene structures is one of the important goals of genome assembly. In low-quality assemblies, and even some high-quality assemblies, certain gene regions are still incomplete; thus, novel scaffolding approaches are required to complete gene regions. Results: We developed an efficient and fast genome scaffolding method called PEP_scaffolder, using proteins to scaffold genomes. The pipeline aims to recover protein-coding gene structures. We tested the method on human contigs; using human UniProt proteins as guides, the improvement on N50 size was 17% increase with an accuracy of similar to 97%. PEP_scaffolder improved the proportion of fully covered proteins among all proteins, which was close to the proportion in the finished genome. The method provided a high accuracy of 91% using orthologs of distant species. Tested on simulated fly contigs, PEP_scaffolder outperformed other scaffolders, with the shortest running time and the highest accuracy.

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