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NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae

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dc.abstract.enNon-coding RNAs (ncRNAs) are major players in the regulation of gene expression. This study analyses seven classes of ncRNAs in plants using sequence and secondary structure-based RNA folding measures. We observe distinct regions in the distribution of AU content along with overlapping regions for different ncRNA classes. Additionally, we find similar averages for minimum folding energy index across various ncRNAs classes except for pre-miRNAs and lncRNAs. Various RNA folding measures show similar trends among the different ncRNA classes except for pre-miRNAs and lncRNAs. We observe different k-mer repeat signatures of length three among various ncRNA classes. However, in pre-miRs and lncRNAs, a diffuse pattern of k-mers is observed. Using these attributes, we train eight different classifiers to discriminate various ncRNA classes in plants. Support vector machines employing radial basis function show the highest accuracy (average F1 of ~96%) in discriminating ncRNAs, and the classifier is implemented as a web server, NCodR.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorBahadur, Ranjit Prasad
dc.contributor.authorBasak, Jolly
dc.contributor.authorMukherjee, Sunandan
dc.contributor.authorChandran, Nithin
dc.date.accessioned2024-01-25T13:31:21Z
dc.date.available2024-01-25T13:31:21Z
dc.date.issued2022
dc.description.financeNie dotyczy
dc.description.volume3
dc.identifier.doi10.1017/QPB.2022.18
dc.identifier.issn2632-8828
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/113448
dc.identifier.weblinkhttps://www.cambridge.org/core/services/aop-cambridge-core/content/view/S2632882822000182
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofQuantitative Plant Biology
dc.relation.pagese23
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.titleNCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae
dc.typeJournalArticle
dspace.entity.typePublication