{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T13:13:36Z","timestamp":1770902016518,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,3,9]],"date-time":"2019-03-09T00:00:00Z","timestamp":1552089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2016YFD0100904"],"award-info":[{"award-number":["2016YFD0100904"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFD1000101"],"award-info":[{"award-number":["2018YFD1000101"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871269"],"award-info":[{"award-number":["31871269"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31571351"],"award-info":[{"award-number":["31571351"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2662017PY043"],"award-info":[{"award-number":["2662017PY043"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence\/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe with these unique features of PAV scanning and building a pan-genome together with its annotation, ppsPCP will be useful for plant pan-genomic studies and aid researchers to study genetic\/phenotypic variations and genomic diversity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The ppsPCP is freely available at github DOI: https:\/\/doi.org\/10.5281\/zenodo.2567390 and webpage http:\/\/cbi.hzau.edu.cn\/ppsPCP\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz168","type":"journal-article","created":{"date-parts":[[2019,3,8]],"date-time":"2019-03-08T12:40:48Z","timestamp":1552048848000},"page":"4156-4158","source":"Crossref","is-referenced-by-count":32,"title":["ppsPCP: a plant presence\/absence variants scanner and pan-genome construction pipeline"],"prefix":"10.1093","volume":"35","author":[{"given":"Muhammad","family":"Tahir Ul Qamar","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics , Huazhong Agricultural University, Wuhan, P. R. China"}]},{"given":"Xitong","family":"Zhu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics , Huazhong Agricultural University, Wuhan, P. R. China"}]},{"given":"Feng","family":"Xing","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics , Huazhong Agricultural University, Wuhan, P. R. China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3005-526X","authenticated-orcid":false,"given":"Ling-Ling","family":"Chen","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics , Huazhong Agricultural University, Wuhan, P. R. China"}]}],"member":"286","published-online":{"date-parts":[[2019,3,9]]},"reference":[{"key":"2023013108272600000_btz168-B1","doi-asserted-by":"crossref","first-page":"421.","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023013108272600000_btz168-B2","doi-asserted-by":"crossref","first-page":"184.","DOI":"10.3389\/fpls.2017.00184","article-title":"Analysis of plant pan-genomes and transcriptomes with GET_HOMOLOGUES-EST, a clustering solution for sequences of the same species","volume":"8","author":"Contreras-Moreira","year":"2017","journal-title":"Front. Plant Sci"},{"key":"2023013108272600000_btz168-B3","doi-asserted-by":"crossref","first-page":"419.","DOI":"10.1038\/nature10414","article-title":"Multiple reference genomes and transcriptomes for Arabidopsis thaliana","volume":"477","author":"Gan","year":"2011","journal-title":"Nature"},{"key":"2023013108272600000_btz168-B4","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/bioinformatics\/bty189","article-title":"scanPAV: a pipeline for extracting presence-absence variations in genome pairs","volume":"1","author":"Giordano","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013108272600000_btz168-B5","doi-asserted-by":"crossref","first-page":"2184.","DOI":"10.1038\/s41467-017-02292-8","article-title":"Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure","volume":"8","year":"2017","journal-title":"Nat. Commun"},{"key":"2023013108272600000_btz168-B6","first-page":"656","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023013108272600000_btz168-B7","doi-asserted-by":"crossref","first-page":"R12.","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"2023013108272600000_btz168-B8","first-page":"506.","article-title":"Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica","volume":"15","author":"Schatz","year":"2014","journal-title":"Genome Biol"},{"key":"2023013108272600000_btz168-B9","doi-asserted-by":"crossref","first-page":"9670.","DOI":"10.1038\/s41598-018-27800-8","article-title":"Pan4Draft: a computational tool to improve the accuracy of pan-genomic analysis using draft genomes","volume":"8","author":"Veras","year":"2018","journal-title":"Sci. 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