Quorum Planted Motif Discovery and Motif Finding Using S2f and Fff Algorithms

Quorum Planted Motif Discovery and Motif Finding Using S2f and Fff Algorithms | 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 Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Quorum Planted Motif Discovery and Motif Finding Using S2f and Fff Algorithms THEEPALAKSHMI sivarajan, SrinivasuluReddy reddy This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1731651/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 20 Oct, 2023 Read the published version in Soft Computing → Version 1 posted 5 You are reading this latest preprint version Abstract A comprehensive understanding of transcription factor binding sites (TFBSs) is a key problem in contemporary biology, which is a critical issue in gene regulation. In the process of identifying a pattern of TFBSs in every DNA sequence, motif discovery reveals the basic regulatory relationship and compassionate the evolutionary system of every species. In this case, however, it is a challenge to recognize the high-quality motif ( ℓ , d) . We intend to address the above problem to the motif discovery and the motif finding using approximate qPMS algorithms such as S2F (Segmentation to Filtration) and FFF (Firefly with FREEZE). To this end, whole DNA sequences are segmented in two sections where the first part is sliced by base and sub k-mers , and the motif is calculated based on the accuracy. The motif that is recognized in the first portion is given as an input to the FFF algorithm to identify the TFBSs locations in the second portion. The algorithm performance is tested on both simulated and real datasets. In particular, real datasets like Escherichia coli cyclic AMP receptor protein(CRP), mouse Embryonic Stem Cell (mESC), and human species ChIP-seq dataset are explored. Results from the experiments show that S2F and FFF algorithms can identify the motifs and appear faster compared to previous state-of-the-art PMS and QPMS algorithms. Planted (ℓ d) Motif Search Motif Discovery Motif Finding Firefly algorithm Freezing technique S2F algorithm Full Text Cite Share Download PDF Status: Published Journal Publication published 20 Oct, 2023 Read the published version in Soft Computing → Version 1 posted Editorial decision: Major Revision 26 May, 2023 Reviewers agreed at journal 01 Jan, 2023 Reviewers invited by journal 12 Dec, 2022 Editor assigned by journal 16 Jun, 2022 First submitted to journal 14 Jun, 2022 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. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies 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-1731651","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":159360991,"identity":"fdcaada9-49b7-424e-9668-875021b2216d","order_by":0,"name":"THEEPALAKSHMI sivarajan","email":"data:image/png;base64,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","orcid":"","institution":"National Institute of Technology Tiruchirappalli","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"THEEPALAKSHMI","middleName":"","lastName":"sivarajan","suffix":""},{"id":159360992,"identity":"b94f6ae8-b9cf-48eb-8f0a-3e3372e7cfab","order_by":1,"name":"SrinivasuluReddy reddy","email":"","orcid":"","institution":"National Institute of Technology Tiruchirappalli","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"SrinivasuluReddy","middleName":"","lastName":"reddy","suffix":""}],"badges":[],"createdAt":"2022-06-06 20:45:18","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-1731651/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-1731651/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00500-023-09236-z","type":"published","date":"2023-10-20T15:01:32+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":45091199,"identity":"5289f276-5207-4083-bb31-445a7f6e410f","added_by":"auto","created_at":"2023-10-23 15:09:07","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":781021,"visible":true,"origin":"","legend":"","description":"","filename":"PAPER3MURFINALS2FFFF2redusimilindex3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1731651/v1_covered_038a3eca-c37e-41a9-bc71-dda9324ff558.pdf"}],"financialInterests":"","formattedTitle":"\u003cp\u003eQuorum Planted Motif Discovery and Motif Finding Using S2f and Fff Algorithms\u003c/p\u003e","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":true,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"soft-computing","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"soco","sideBox":"Learn more about [Soft Computing](https://www.springer.com/journal/500)","snPcode":"500","submissionUrl":"https://submission.nature.com/new-submission/500/3","title":"Soft Computing","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Planted (ℓ, d) Motif Search; Motif Discovery, Motif Finding, Firefly algorithm, Freezing technique, S2F algorithm","lastPublishedDoi":"10.21203/rs.3.rs-1731651/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1731651/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"A comprehensive understanding of transcription factor binding sites (TFBSs) is a key problem in contemporary biology, which is a critical issue in gene regulation. 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