{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T17:08:48Z","timestamp":1732036128392},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,26]],"date-time":"2016-10-26T00:00:00Z","timestamp":1477440000000},"content-version":"vor","delay-in-days":126,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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 \u223c97%. 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.<\/jats:p>\n               <jats:p>Availability and Implementation: The software is freely available at http:\/\/www.fishbrowser.org\/software\/PEP_scaffolder\/<\/jats:p>\n               <jats:p>Contact: \u00a0lijt@cafs.ac.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw378","type":"journal-article","created":{"date-parts":[[2016,6,24]],"date-time":"2016-06-24T05:19:32Z","timestamp":1466745572000},"page":"3193-3195","source":"Crossref","is-referenced-by-count":14,"title":["PEP_scaffolder: using (homologous) proteins to scaffold genomes"],"prefix":"10.1093","volume":"32","author":[{"given":"Bai-Han","family":"Zhu","sequence":"first","affiliation":[{"name":"1 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China"},{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying-Nan","family":"Song","sequence":"additional","affiliation":[{"name":"1 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China"},{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Xue","sequence":"additional","affiliation":[{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gui-Cai","family":"Xu","sequence":"additional","affiliation":[{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"},{"name":"3 College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Xiao","sequence":"additional","affiliation":[{"name":"1 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China"},{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming-Yuan","family":"Sun","sequence":"additional","affiliation":[{"name":"1 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China"},{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao-Wen","family":"Sun","sequence":"additional","affiliation":[{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiong-Tang","family":"Li","sequence":"additional","affiliation":[{"name":"2 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,6,22]]},"reference":[{"key":"2023020113472825100_btw378-B1","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gks1195","article-title":"GenBank","volume":"41","author":"Benson","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020113472825100_btw378-B2","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1101\/gr.1865504","article-title":"GeneWise and Genomewise","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"key":"2023020113472825100_btw378-B3","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information","volume":"43","author":"Consortium","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020113472825100_btw378-B4","doi-asserted-by":"crossref","first-page":"D662","DOI":"10.1093\/nar\/gku1010","article-title":"Ensembl 2015","volume":"43","author":"Cunningham","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020113472825100_btw378-B5","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1093\/bib\/bbr038","article-title":"Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)","volume":"12","author":"Dessimoz","year":"2011","journal-title":"Brief. 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