title: PEP_scaffolder: using (homologous) proteins to scaffold genomes.
abstract: 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.
  
  
  
  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 ∼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.
  
  
  
  The software is freely available at http://www.fishbrowser.org/software/PEP_scaffolder/ CONTACT: lijt@cafs.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Bai-Han
authors.initials: BH
authors.lastname: Zhu
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Ying-Nan
authors.initials: YN
authors.lastname: Song
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xue
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China.
authors.forename: Gui-Cai
authors.initials: GC
authors.lastname: Xu
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Xiao
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Ming-Yuan
authors.initials: MY
authors.lastname: Sun
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Xiao-Wen
authors.initials: XW
authors.lastname: Sun
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
mesh_terms: D000465:Algorithms; D000818:Animals; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012984:Software