Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/150965
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dc.contributor.authorLe, Nguyen Quoc Khanhen_US
dc.contributor.authorYapp, Edward Kien Yeeen_US
dc.contributor.authorHo, Quang-Thaien_US
dc.contributor.authorNagasundaram, Nagarajanen_US
dc.contributor.authorOu, Yu-Yenen_US
dc.contributor.authorYeh, Hui-Yuanen_US
dc.date.accessioned2021-05-31T08:16:39Z-
dc.date.available2021-05-31T08:16:39Z-
dc.date.issued2019-
dc.identifier.citationLe, N. Q. K., Yapp, E. K. Y., Ho, Q., Nagasundaram, N., Ou, Y. & Yeh, H. (2019). iEnhancer-5step : identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding. Analytical Biochemistry, 571, 53-61. https://dx.doi.org/10.1016/j.ab.2019.02.017en_US
dc.identifier.issn0003-2697en_US
dc.identifier.urihttps://hdl.handle.net/10356/150965-
dc.description.abstractAn enhancer is a short (50–1500bp) region of DNA that plays an important role in gene expression and the production of RNA and proteins. Genetic variation in enhancers has been linked to many human diseases, such as cancer, disorder or inflammatory bowel disease. Due to the importance of enhancers in genomics, the classification of enhancers has become a popular area of research in computational biology. Despite the few computational tools employed to address this problem, their resulting performance still requires improvements. In this study, we treat enhancers by the word embeddings, including sub-word information of its biological words, which then serve as features to be fed into a support vector machine algorithm to classify them. We present iEnhancer-5Step, a web server containing two-layer classifiers to identify enhancers and their strength. We are able to attain an independent test accuracy of 79% and 63.5% in the two layers, respectively. Compared to current predictors on the same dataset, our proposed method is able to yield superior performance as compared to the other methods. Moreover, this study provides a basis for further research that can enrich the field of applying natural language processing techniques in biological sequences. iEnhancer-5Step is freely accessible via http://biologydeep.com/fastenc/.en_US
dc.description.sponsorshipNanyang Technological Universityen_US
dc.language.isoenen_US
dc.relation.ispartofAnalytical Biochemistryen_US
dc.rights© 2019 Elsevier Inc. All rights reserved.en_US
dc.subjectScience::Biological sciencesen_US
dc.titleiEnhancer-5step : identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embeddingen_US
dc.typeJournal Articleen
dc.contributor.schoolSchool of Humanitiesen_US
dc.identifier.doi10.1016/j.ab.2019.02.017-
dc.identifier.pmid30822398-
dc.identifier.scopus2-s2.0-85062237812-
dc.identifier.volume571en_US
dc.identifier.spage53en_US
dc.identifier.epage61en_US
dc.subject.keywordsSkip Gramen_US
dc.subject.keywordsContinuous Bag of Wordsen_US
dc.description.acknowledgementThis work has been supported by the Nanyang Technological University Start-Up Grant.en_US
item.fulltextNo Fulltext-
item.grantfulltextnone-
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