Cov-trans: An Efficient Algorithm for Discontinuous Transcript Assembly in Coronaviruses

Cov-trans: An Efficient Algorithm for Discontinuous Transcript Assembly in Coronaviruses | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Cov-trans: An Efficient Algorithm for Discontinuous Transcript Assembly in Coronaviruses Xiaoyu Guo, Zhenming Wu, Shu Zhang, Jin Zhao This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5209327/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 30 Dec, 2024 Read the published version in BMC Genomics → Version 1 posted 14 You are reading this latest preprint version Abstract Background: Discontinuous transcription allows coronaviruses to efficiently replicate and transmit within host cells, enhancing their adaptability and survival. Assembling viral transcripts is crucial for virology research and the development of antiviral strategies. However, traditional transcript assembly methods primarily designed for variable alternative splicing events in eukaryotes are not suitable for the viral transcript assembly problem. The current algorithms designed for assembling viral transcripts often struggle with low accuracy in determining the transcript boundaries. There is an urgent need to develop a highly accurate viral transcript assembly algorithm. Results: In this work, we propose Cov-trans, a reference-based transcript assembler specifically tailored for the discontinuous transcription of coronaviruses. Cov-trans first identifies canonical transcripts based on discontinuous transcription mechanisms, start and stop codons, as well as reads alignment information. Subsequently, it formulates the assembly of non-canonical transcripts as a path extraction problem, and introduces a mixed integer linear programming to recover these non-canonical transcripts. Conclusion: Experimental results show that Cov-trans outperforms other assemblers in both accuracy and recall, with a notable strength in accurately identifying the boundaries of transcripts. Cov-trans is freely available at https://github.com/computer-Bioinfo/Cov-trans. referenced-based assembly mixed integer linear programming discontinuous transcription coronaviruses Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 30 Dec, 2024 Read the published version in BMC Genomics → Version 1 posted Editorial decision: Revision requested 02 Dec, 2024 Reviews received at journal 28 Nov, 2024 Reviewers agreed at journal 23 Nov, 2024 Reviewers agreed at journal 23 Nov, 2024 Reviews received at journal 30 Oct, 2024 Reviewers agreed at journal 24 Oct, 2024 Reviewers agreed at journal 18 Oct, 2024 Reviewers agreed at journal 18 Oct, 2024 Reviewers agreed at journal 18 Oct, 2024 Reviewers invited by journal 17 Oct, 2024 Editor invited by journal 16 Oct, 2024 Editor assigned by journal 09 Oct, 2024 Submission checks completed at journal 09 Oct, 2024 First submitted to journal 05 Oct, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5209327","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":385357462,"identity":"5126615e-efd0-41c7-8dea-ec38c17c308a","order_by":0,"name":"Xiaoyu Guo","email":"","orcid":"","institution":"Qingdao University","correspondingAuthor":false,"prefix":"","firstName":"Xiaoyu","middleName":"","lastName":"Guo","suffix":""},{"id":385357468,"identity":"43f3f51b-d69e-48f0-819f-59ebbfee43aa","order_by":1,"name":"Zhenming Wu","email":"","orcid":"","institution":"Qingdao University","correspondingAuthor":false,"prefix":"","firstName":"Zhenming","middleName":"","lastName":"Wu","suffix":""},{"id":385357470,"identity":"17a0b37b-87bc-44e6-9132-2ee0999e9faa","order_by":2,"name":"Shu Zhang","email":"","orcid":"","institution":"Qingdao University","correspondingAuthor":false,"prefix":"","firstName":"Shu","middleName":"","lastName":"Zhang","suffix":""},{"id":385357471,"identity":"624720ed-2581-49a5-a3f8-2a0c42e74792","order_by":3,"name":"Jin Zhao","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0UlEQVRIiWNgGAWjYDACCRA2YJBjYEgAsthI0GJMohYgSGwgWov87OaHDywK7qT3Hc8xYPhQdpiBf3YDfi2Mc44ZG0gYPMudeeaNAeOMc4cZJO4cwK+FWSLBTELC4HDuhhs5Bsy8bYcZDCQS8Gthk0j/BtKSbgDS8pcYLTwSOWBbEsBaGInRIiGRUwz0y2HDmWeeFRzsOZfOI3GDgBb5GekbH0v8OSzPdzx544MfZdZy/DMIaAEBZnDcHAAjBh7C6oGA8QNUyygYBaNgFIwCrAAASShBt09jT68AAAAASUVORK5CYII=","orcid":"","institution":"Qingdao University","correspondingAuthor":true,"prefix":"","firstName":"Jin","middleName":"","lastName":"Zhao","suffix":""}],"badges":[],"createdAt":"2024-10-05 14:23:09","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5209327/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5209327/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12864-024-11179-0","type":"published","date":"2024-12-30T15:57:26+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":73093482,"identity":"b5902416-6907-4b5a-8801-5f1b2df97170","added_by":"auto","created_at":"2025-01-06 16:20:46","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2086812,"visible":true,"origin":"","legend":"","description":"","filename":"Covtransbmcgenomics3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5209327/v1_covered_20096d10-b1d5-4497-a32c-b323dac75be2.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Cov-trans: An Efficient Algorithm for Discontinuous Transcript Assembly in Coronaviruses","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"referenced-based assembly, mixed integer linear programming, discontinuous transcription, coronaviruses","lastPublishedDoi":"10.21203/rs.3.rs-5209327/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5209327/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDiscontinuous transcription allows coronaviruses to efficiently replicate and transmit within host cells, enhancing their adaptability and survival. Assembling viral transcripts is crucial for virology research and the development of antiviral strategies. However, traditional transcript assembly methods primarily designed for variable alternative splicing events in eukaryotes are not suitable for the viral transcript assembly problem. The current algorithms designed for assembling viral transcripts often struggle with low accuracy in determining the transcript boundaries. There is an urgent need to develop a highly accurate viral transcript assembly algorithm.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIn this work, we propose Cov-trans, a reference-based transcript assembler specifically tailored for the discontinuous transcription of coronaviruses. Cov-trans first identifies canonical transcripts based on discontinuous transcription mechanisms, start and stop codons, as well as reads alignment information. 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