[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-125166-en":3,"doc-seo-125166-105":30,"detail-sidebar-cat-0-en-105":91},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":4,"category_id":11,"category_name":12,"doc_title":13,"doc_description":14,"doc_content":15,"file_id":16,"file_url":17,"file_type":18,"file_size":19,"view_count":4,"is_deleted":4,"is_public":20,"is_downloadable":20,"audit_status":20,"page_count":21,"language":22,"language_code":23,"site_id":24,"html_lang":23,"table_of_contents":25,"faqs":26,"seo_title":27,"seo_description":14,"update_tm":28,"read_time":29},125166,13056703019404,"Miles","https://ap-avatar.wpscdn.com/davatar_29158cc5080c5b710cf443261637dec0",8,"Research & Report","PlasmidHunter - accurate and fast prediction of plasmid sequences","Plasmids are extrachromosomal DNA in microorganisms that often carry genes enabling bacterial adaptation to harsh environments, and they are crucial in genetic engineering, gene therapy, and drug production. Identifying plasmid sequences from chromosomal data in genomic and metagenomic datasets remains challenging. PlasmidHunter is a machine-learning tool that predicts plasmid sequences using a gene content profile, delivering high accuracy (up to 97.6%) and high speed on benchmark tests with both simulated contigs and real metagenomic plasmidome data, outperforming existing tools.","Lawrence Berkeley National Laboratory  \nLBL Publications  \nTitle  \nPlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning.  \nPermalink  \n[https://escholarship.org/uc/item/0hf88646](https://escholarship.org/uc/item/0hf88646)  \nJournal  \nBriefings in Bioinformatics, 25(4)  \nAuthors  \nTian, Renmao  \nZhou, Jizhong Imanian, Behzad  \nPublication Date  \n2024-05-23  \nDOI  \n10.1093/bib/bbae322  \nPeer reviewed  \n[eScholarship.org](eScholarship.org) Powered by the California Digital Library  \nUniversity of California  \nBriefings in Bioinformatics, 2024, 25(4), bbae322  \n[https://doi.org/10.1093/bib/bbae322](https://doi.org/10.1093/bib/bbae322)  \nProblem Solving Protocol  \nPlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning  \nRenmao Tian 1 , Jizhong Zhou2 , Behzad Imanian 1 , 3 , *  \n1 Institute for Food Safety and Health, Illinois Institute of Technology, 6502 S Archer Rd, Bedford Park, IL 60501, United States  \n2 Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, 101 David L Boren Blvd, Norman, OK 73019, United States  \n3 Food Science and Nutrition Department, Illinois Institute of Technology, 10 West 35th Street, Chicago, IL 60616, United States  \n*Corresponding author. Institute for Food Safety and Health, Illinois Institute of Technology, 6502 S Archer Rd, Bedford Park, IL 60501, United States. [E-mail: bimanian@iit.edu](E-mail: bimanian@iit.edu)  \nAbstract  \nPlasmids are extrachromosomal DNA found in microorganisms. They often carry beneficial genes that help bacteria adapt to harsh conditions. Plasmids are also important tools in genetic engineering, gene therapy, and drug production. However, it can be difficult to identify plasmid sequences from chromosomal sequences in genomic and metagenomic data. Here, we have developed a new tool called PlasmidHunter, which uses machine learning to predict plasmid sequences based on gene content profile. PlasmidHunter can achieve high accuracies (up to 97.6%) and high speeds in benchmark tests including both simulated contigs and real metagenomic plasmidome data, outperforming other existing tools.  \nKeywords: artificial intelligence (AI); machine learning (ML); plasmid prediction; genomic sequencing  \nBackground  \nPlasmids are extrachromosomal and transmissible segments of naked, double-stranded DNA that, unlike viruses, replicate autonomously within a host cell. They are common in bacteria, but they are also found in archaea and eukaryota. Plasmids are typically circular and often much smaller than chromosomes, but their sizes vary considerably (from ∼1 kbp to >1 Mbp) [1–3] .  \nAs agents of horizontal gene transfer (HGT) between bacterial species [4], plasmids spread the traits that might influence the characteristics, survival, and fitness of the hosts, and thus they play an important role in the bacterial evolution and ecology. Plasmids carry non-essential and sometimes beneficial genes  \nthat help their hosts tolerate and survive hostile conditions ina changing environment. For example, a plasmid-borne gene encodes the mercuric reductase that converts toxic Hg2+ to a volatile and less toxic metallic Hg0 [5] . We now know that plasmids play a key role in spreading the antimicrobial resistance genes (ARGs) among the related bacterial species [6–8], such as those conferring resistance to many commonly used antibiotics such as tetracycline and penicillin or to β-lactams (bla) [9] and aminoglycosides (aad and aac) [10] . In addition to transferring antimicrobial resistance (AMR) to other bacteria, plasmids can transmit and spread other traits [4] such as virulence, toxicity, and pathogenicity to a wider group of bacteria, and consequently, they  \nRenmao Tian (Tim) is a leading research scientist at the Institute for Food Safety and Health, Illinois Institute of Technology. With interdisciplinary expertise in bioinformat","cbCaii7wDFWq0zDJ","https://ap.wps.com/l/cbCaii7wDFWq0zDJ","pdf",1112162,1,10,"English","en",105,"# Abstract\n# Background\n## Plasmids and horizontal gene transfer\n## Importance in adaptation and antimicrobial resistance\n# Method: PlasmidHunter overview\n# Performance highlights","[{\"question\":\"What problem does PlasmidHunter address?\",\"answer\":\"It addresses the difficulty of identifying plasmid sequences from chromosomal sequences in genomic and metagenomic data.\"},{\"question\":\"How does PlasmidHunter make predictions?\",\"answer\":\"It uses machine learning to predict plasmid sequences based on a gene content profile.\"},{\"question\":\"What performance does PlasmidHunter achieve in benchmarks?\",\"answer\":\"On benchmark tests using simulated contigs and real metagenomic plasmidome data, it reaches high accuracies up to 97.6% and high speeds, outperforming existing tools.\"}]","PlasmidHunter - accurate and fast prediction of plasmid sequences | PDF",1785897091,25,{"code":4,"msg":31,"data":32},"ok",{"site_id":24,"language":23,"slug":33,"title":13,"keywords":34,"description":14,"schema_data":35,"social_meta":86,"head_meta":88,"extra_data":90,"updated_unix":28},"plasmidhunter-accurate-and-fast-prediction-of-plasmid-sequences","",{"@graph":36,"@context":85},[37,54,68],{"@type":38,"itemListElement":39},"BreadcrumbList",[40,44,48,51],{"item":41,"name":42,"@type":43,"position":20},"https://docshare.wps.com","Home","ListItem",{"item":45,"name":46,"@type":43,"position":47},"https://docshare.wps.com/document/","Document",2,{"item":49,"name":12,"@type":43,"position":50},"https://docshare.wps.com/document/research-report/",3,{"item":52,"name":13,"@type":43,"position":53},"https://docshare.wps.com/document/plasmidhunter-accurate-and-fast-prediction-of-plasmid-sequences/125166/",4,{"url":52,"name":13,"@type":55,"author":56,"headline":13,"publisher":58,"fileFormat":61,"inLanguage":23,"description":14,"dateModified":62,"datePublished":62,"encodingFormat":61,"isAccessibleForFree":63,"interactionStatistic":64},"DigitalDocument",{"name":9,"@type":57},"Person",{"url":41,"name":59,"@type":60},"DocShare","Organization","application/pdf","2026-08-05",true,{"@type":65,"interactionType":66,"userInteractionCount":4},"InteractionCounter",{"@type":67},"ViewAction",{"@type":69,"mainEntity":70},"FAQPage",[71,77,81],{"name":72,"@type":73,"acceptedAnswer":74},"What problem does PlasmidHunter address?","Question",{"text":75,"@type":76},"It addresses the difficulty of identifying plasmid sequences from chromosomal sequences in genomic and metagenomic data.","Answer",{"name":78,"@type":73,"acceptedAnswer":79},"How does PlasmidHunter make predictions?",{"text":80,"@type":76},"It uses machine learning to predict plasmid sequences based on a gene content profile.",{"name":82,"@type":73,"acceptedAnswer":83},"What performance does PlasmidHunter achieve in benchmarks?",{"text":84,"@type":76},"On benchmark tests using simulated contigs and real metagenomic plasmidome data, it reaches high accuracies up to 97.6% and high speeds, outperforming existing tools.","https://schema.org",{"og:url":52,"og:type":87,"og:title":13,"og:site_name":59,"og:description":14},"article",{"robots":89,"canonical":52},"index,follow",{"doc_id":7,"site_id":24},{"code":4,"msg":5,"data":92},[93,97,101,105,110,115,120,123,128,131,134],{"id":20,"doc_module":4,"doc_module_name":46,"category_name":94,"show_sort_weight":95,"slug":96},"Story & Novel",90,"story-novel",{"id":47,"doc_module":4,"doc_module_name":46,"category_name":98,"show_sort_weight":99,"slug":100},"Literature",80,"literature",{"id":53,"doc_module":4,"doc_module_name":46,"category_name":102,"show_sort_weight":103,"slug":104},"Exam",70,"exam",{"id":106,"doc_module":4,"doc_module_name":46,"category_name":107,"show_sort_weight":108,"slug":109},5,"Comic",60,"comic",{"id":111,"doc_module":4,"doc_module_name":46,"category_name":112,"show_sort_weight":113,"slug":114},6,"Technology",50,"technology",{"id":116,"doc_module":4,"doc_module_name":46,"category_name":117,"show_sort_weight":118,"slug":119},7,"Healthcare",40,"healthcare",{"id":11,"doc_module":4,"doc_module_name":46,"category_name":12,"show_sort_weight":121,"slug":122},30,"research-report",{"id":124,"doc_module":4,"doc_module_name":46,"category_name":125,"show_sort_weight":126,"slug":127},9,"Religion & Spirituality",20,"religion-spirituality",{"id":126,"doc_module":4,"doc_module_name":46,"category_name":129,"show_sort_weight":126,"slug":130},"World Cup","world-cup",{"id":21,"doc_module":4,"doc_module_name":46,"category_name":132,"show_sort_weight":21,"slug":133},"Lifestyle","lifestyle",{"id":135,"doc_module":4,"doc_module_name":46,"category_name":136,"show_sort_weight":106,"slug":137},19,"General","general"]