Separating Phages From Other Virus Families and Classifying the Different Phage Families By GI-Clusters

Separating Phages From Other Virus Families and Classifying the Different Phage Families By GI-Clusters | 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 Separating Phages From Other Virus Families and Classifying the Different Phage Families By GI-Clusters Xingang Jia, Qiuhong Han, Zuhong Lu This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1130357/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background : Phages are the most abundant biological entities, but the commonly used clustering techniques are difficult to separate them from other virus families and classify the different phage families together. Results : This work uses GI -clusters to separate phages from other virus families and classify the different phage families, where GI -clusters are constructed by GI -features, GI -features are constructed by the togetherness with F -features, training data, MG-Euclidean and Icc-cluster algorithms, F -features are the frequencies of multiple-nucleotides that are generated from genomes of viruses, MG -Euclidean algorithm is able to put the nearest neighbors in the same mini-groups, and Icc-cluster algorithm put the distant samples to the different mini-clusters. For these viruses that the maximum element of their GI -features are in the same locations, they are put to the same GI -clusters, where the families of viruses in test data are identified by GI -clusters, and the families of GI -clusters are defined by viruses of training data. Conclusions : From analysis of 4 data sets that are constructed by the different family viruses, we demonstrate that GI -clusters are able to separate phages from other virus families, correctly classify the different phage families, and correctly predict the families of these unknown phages also. Computational Biology Bioinformatics Cellular & Molecular Neuroscience MG-Euclidean Icc-cluster F-feature GI-feature GI-cluster Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Full Text Additional Declarations No competing interests reported. Supplementary Files Additionalfile1.xlsx the details of Data-s, training-s and test-s. Cite Share Download PDF Status: Posted Version 1 posted 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-1130357","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":67737907,"identity":"8fde23f0-622d-416b-9609-cc41434fa6c7","order_by":0,"name":"Xingang Jia","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAsklEQVRIiWNgGAWjYBACAyBmZjD4J8fG3n6AFC0FB4z5eM4kkKLlw4HEeRIOBsRpMWc/e/B2gcGd9DYJhgSGHxXbCGux7MlLtp5h8Cy3TbrxAGPPmdtEOOxAjpk0jwFzbpvMgQRmxjZitJx/A9aSziaRYECklhtgWw4nkKLljbE1j0GaYRswkA8S55fzOYa3ef7YyMu3tx988KOCCC0gIAFjHCBOPbKWUTAKRsEoGAVYAQD19DpAtkHNvAAAAABJRU5ErkJggg==","orcid":"","institution":"Southeast University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Xingang","middleName":"","lastName":"Jia","suffix":""},{"id":67737908,"identity":"dc6018ce-7757-4158-8ef2-0d42a543e516","order_by":1,"name":"Qiuhong Han","email":"","orcid":"","institution":"Nanjing Forestry University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Qiuhong","middleName":"","lastName":"Han","suffix":""},{"id":67737910,"identity":"f6eb001d-8c98-4c73-b10f-d31eec21f2d1","order_by":2,"name":"Zuhong Lu","email":"","orcid":"","institution":"Southeast University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Zuhong","middleName":"","lastName":"Lu","suffix":""}],"badges":[],"createdAt":"2021-12-01 07:29:11","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-1130357/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-1130357/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":16221581,"identity":"8ce9aa2b-0b48-4512-aa95-497eac8597c5","added_by":"auto","created_at":"2021-12-06 18:00:31","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":124337,"visible":true,"origin":"","legend":"The t-SNE maps of virus of data-s, where t-SNE maps were generated from\nF4-features, and viruses were colored according to their families. (a) The t-SNE maps of 10 D1,l-clusters. (b) The t-SNE maps of 6 D2,l-clusters. (c) The t-SNE maps of 9 D3,l-clusters. (d) The t-SNE maps of 4 D4,l-clusters.","description":"","filename":"Fig1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1/e3a8a71f6a8c325667c5224b.jpg"},{"id":16221583,"identity":"ef49817e-9df6-4c95-b5c2-0e1d0e20e1ae","added_by":"auto","created_at":"2021-12-06 18:00:31","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":114651,"visible":true,"origin":"","legend":"The t-SNE maps of viruses of data-s, where t-SNE maps were generated from\nG-features, and viruses were colored according to their families. (a) The t-SNE maps of 10 D1,l-clusters. (b) The t-SNE maps of 6 D2,l-clusters. (c) The t-SNE maps of 9 D3,l-clusters. (d) The t-SNE maps of 4 D4,l-clusters.","description":"","filename":"Fig2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1/156dffdab68237018a8eba56.jpg"},{"id":16221584,"identity":"07822397-74e6-4de1-95e8-679ae8eec8f9","added_by":"auto","created_at":"2021-12-06 18:00:31","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":115527,"visible":true,"origin":"","legend":"The t-SNE maps of viruses of data-s, where t-SNE maps were generated from\nI-features, and viruses were colored according to their families. (a) The t-SNE maps of 10 D1,l-clusters. (b) The t-SNE maps of 6 D2,l-clusters. (c) The t-SNE maps of 9 D3,l-clusters. (d) The t-SNE maps of 4 D4,l-clusters.","description":"","filename":"Fig3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1/80094d2f8c041636afd7d1ad.jpg"},{"id":16221582,"identity":"92c8365d-469f-438e-9e26-e9af4ad5681b","added_by":"auto","created_at":"2021-12-06 18:00:31","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":120644,"visible":true,"origin":"","legend":"The t-SNE maps of viruses of data-s, where t-SNE maps were generated from\nGI-features, and viruses were colored according to their families. (a) The t-SNE maps of 10 D1,l-clusters. (b) The t-SNE maps of 6 D2,l-clusters. (c) The t-SNE maps of 9 D3,l-clusters. (d) The t-SNE maps of 4 D4,l-clusters.","description":"","filename":"Fig4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1/1428b92629ff78cd2ba69319.jpg"},{"id":16221884,"identity":"4385149d-002e-4c07-aa85-e3ba6a6eeb5f","added_by":"auto","created_at":"2021-12-06 18:03:31","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":247271,"visible":true,"origin":"","legend":"The pro\fle plots of G-features, I-features and GI-features of 6 D2,l-clusters, where\nthe X-axis represented the positions of the feature components, the Y-axis represented the value of the feature components. (a1), (b1) and (c1) The pro\fles of G-features, I-features and GI-features of D2,1-cluster. (a2), (b2) and (c2) The pro\fles of G-features, I-features and GI-features of D2,2-cluster. (a3), (b3) and (c3) The pro\fles of G-features, I-features and GI-features of D2,3-cluster. (a4), (b4) and (c4) The pro\fles of G-features, I-features and GI-features of D2,4-cluster. (a5), (b5) and (c5) The pro\fles of G-features, I-features and GI-features of D2,5-cluster. (a6), (b6) and (c6) The pro\fles of G-features, I-features and GI-features of D2,6-cluster.","description":"","filename":"Fig5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1/b84ec62b22e4b97aee76b219.jpg"},{"id":18022251,"identity":"5adcd5e1-1ac5-4d83-9fb9-24693ad50a09","added_by":"auto","created_at":"2022-02-08 08:14:39","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":661651,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscriptfile.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1_covered.pdf"},{"id":16221912,"identity":"d8c19fc9-3e01-4e48-a106-c91af9d2919e","added_by":"auto","created_at":"2021-12-06 18:03:36","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":592707,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscriptfile.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1_covered.pdf"},{"id":16221580,"identity":"5dba6ce3-47f5-4743-8491-ff6576865065","added_by":"auto","created_at":"2021-12-06 18:00:31","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":30518,"visible":true,"origin":"","legend":"the details of Data-s, training-s and test-s.","description":"","filename":"Additionalfile1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1130357/v1/1da2bc69d45ec998194d59ac.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"\u003cp\u003eSeparating Phages From Other Virus Families and Classifying the Different Phage Families By GI-Clusters\u003c/p\u003e","fulltext":[{"header":"Full Text","content":"This preprint is available for \u003ca href='/article/rs-1130357/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e."}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"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":"MG-Euclidean, Icc-cluster, F-feature, GI-feature, GI-cluster","lastPublishedDoi":"10.21203/rs.3.rs-1130357/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1130357/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e: Phages are the most abundant biological entities, but the commonly used clustering techniques are difficult to separate them from other virus families and classify the different phage families together.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e: This work uses \u003cem\u003eGI\u003c/em\u003e-clusters to separate phages from other virus families and classify the different phage families, where \u003cem\u003eGI\u003c/em\u003e-clusters are constructed by \u003cem\u003eGI\u003c/em\u003e-features, \u003cem\u003eGI\u003c/em\u003e-features are constructed by the togetherness with \u003cem\u003eF\u003c/em\u003e-features, training data, MG-Euclidean and Icc-cluster algorithms, \u003cem\u003eF\u003c/em\u003e-features are the frequencies of multiple-nucleotides that are generated from genomes of viruses, \u003cem\u003eMG\u003c/em\u003e-Euclidean algorithm is able to put the nearest neighbors in the same mini-groups, and Icc-cluster algorithm put the distant samples to the different mini-clusters. For these viruses that the maximum element of their \u003cem\u003eGI\u003c/em\u003e-features are in the same locations, they are put to the same \u003cem\u003eGI\u003c/em\u003e-clusters, where the families of viruses in test data are identified by \u003cem\u003eGI\u003c/em\u003e-clusters, and the families of \u003cem\u003eGI\u003c/em\u003e-clusters are defined by viruses of training data.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e: From analysis of 4 data sets that are constructed by the different family viruses, we demonstrate that \u003cem\u003eGI\u003c/em\u003e-clusters are able to separate phages from other virus families, correctly classify the different phage families, and correctly predict the families of these unknown phages also.\u003c/p\u003e","manuscriptTitle":"Separating Phages From Other Virus Families and Classifying the Different Phage Families By GI-Clusters","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2021-12-06 18:00:29","doi":"10.21203/rs.3.rs-1130357/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","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}}],"origin":"","ownerIdentity":"ff477b99-b75b-4566-8a6b-3624ebcba3be","owner":[],"postedDate":"December 6th, 2021","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":8970199,"name":"Computational Biology"},{"id":8970200,"name":"Bioinformatics"},{"id":8970201,"name":"Cellular \u0026 Molecular Neuroscience"}],"tags":[],"updatedAt":"2022-02-08T08:14:25+00:00","versionOfRecord":[],"versionCreatedAt":"2021-12-06 18:00:29","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-1130357","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-1130357","identity":"rs-1130357","version":["v1"]},"buildId":"7rjqhiLT3MXkJMwkYKINL","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}