Data recovery methods for DNA storage based on fountain codes

Data recovery methods for DNA storage based on fountain codes | 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 Article Data recovery methods for DNA storage based on fountain codes Peter Schwarz, Bernd Freisleben This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3252364/v2 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 01 Apr, 2024 Read the published version in Computational and Structural Biotechnology Journal → Version 2 posted You are reading this latest preprint version Show more versions Abstract Today’s digital data storage systems typically offer advanced data recovery solutions for the problem of catastrophic data loss. For conventional hard disk drives, several data recovery mechanisms are available, ranging from software-based disk sector or file analysis to physicallevel data retrieval methods. In contrast, DNA-based data storage exclusively relies on the inherent error correction properties of the encoding methods employed to encode digital data into strands of DNA. In this article, we propose a novel approach to provide data recovery in DNA storage systems. In particular, we present a novel method to automatically reconstruct original data from corrupted data stored and encoded in DNA using fountain codes. Our method exploits the intrinsic relationships between processed packets encoded with fountain codes to identify and rectify errors. Furthermore, we present file type-specific and contentbased error detection and correction methods for three file types, illustrating how a fusion of fountain encoding-specific redundancy and knowledge about the stored data can effectively recover information in a partially corrupted DNA storage system, both in an automatic and in a guided manual manner. To demonstrate the feasibility of our approach, we introduce DR4DNA, a software toolkit that contains all methods presented in this work. Compared to conventional DNA error correction schemes, our approach introduces a fallback recovery approach similar to data recovery services for hard drives. We evaluate DR4DNA using both in-silico and in-vitro experiments. Biological sciences/Computational biology and bioinformatics/Computational platforms and environments Biological sciences/Computational biology and bioinformatics Biological sciences/Computational biology and bioinformatics/Software Biological sciences/Systems biology/DNA computing and cryptography Biological sciences/Systems biology/Computer science fountain codes data recovery reconstruction DNA storage DNA data forensics Full Text Additional Declarations The authors declare no competing interests. Supplementary Files supplement.pdf Cite Share Download PDF Status: Published Journal Publication published 01 Apr, 2024 Read the published version in Computational and Structural Biotechnology Journal → Version 2 posted You are reading this latest preprint version Show more versions 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-3252364","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":228018385,"identity":"210cbf84-1338-4d4e-b9d5-5bcda9d8c874","order_by":0,"name":"Peter Schwarz","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0001-8763-1507","institution":"Philipps-University of Marburg","correspondingAuthor":true,"prefix":"","firstName":"Peter","middleName":"","lastName":"Schwarz","suffix":""},{"id":228018386,"identity":"4bed1711-4843-4bd2-9cbf-e526669fc9bb","order_by":1,"name":"Bernd Freisleben","email":"","orcid":"https://orcid.org/0000-0002-7205-8389","institution":"Philipps-University of Marburg","correspondingAuthor":false,"prefix":"","firstName":"Bernd","middleName":"","lastName":"Freisleben","suffix":""}],"badges":[],"createdAt":"2023-08-10 13:02:18","currentVersionCode":2,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-3252364/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-3252364/v2","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1016/j.csbj.2024.04.048","type":"published","date":"2024-04-01T22:03:10+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":55335119,"identity":"623d85f8-a3f0-4422-abd7-ab3c6d8bdf48","added_by":"auto","created_at":"2024-04-25 22:03:18","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":626407,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3252364/v2_covered_9d7d4bbd-48ec-48de-b906-46408126e048.pdf"},{"id":50457409,"identity":"eab626d7-4337-4803-b27a-31ab7a669cb9","added_by":"auto","created_at":"2024-01-31 19:33:22","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":80882,"visible":true,"origin":"","legend":"","description":"","filename":"supplement.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3252364/v2/b9c976a4e50820b652fcd3f4.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"Data recovery methods for DNA storage based on fountain codes","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"fountain codes, data recovery, reconstruction, DNA storage, DNA, data forensics","lastPublishedDoi":"10.21203/rs.3.rs-3252364/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3252364/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eToday’s digital data storage systems typically offer advanced data recovery solutions for the problem of catastrophic data loss. 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