RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery

Summary: Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using an ultra-fast inexact k-mers search for stati...

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Autores principales:	Nitesh Kumar Sharma, Sagar Gupta, Ashwani Kumar, Prakash Kumar, Upendra Kumar Pradhan, Ravi Shankar
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Sequence analysis Systems biology Omics Science Q
Acceso en línea:	https://doaj.org/article/6f67ca246bed473b92c2e7b266e6a876
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id	oai:doaj.org-article:6f67ca246bed473b92c2e7b266e6a876
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spelling	oai:doaj.org-article:6f67ca246bed473b92c2e7b266e6a8762021-11-18T04:51:11ZRBPSpot: Learning on appropriate contextual information for RBP binding sites discovery2589-004210.1016/j.isci.2021.103381https://doaj.org/article/6f67ca246bed473b92c2e7b266e6a8762021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2589004221013523https://doaj.org/toc/2589-0042Summary: Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using an ultra-fast inexact k-mers search for statistically significant seeds. The seeds work as an anchor to evaluate the context and binding potential using flanking region information while leveraging from Deep Feed-forward Neural Network. The developed models also received support from MD-simulation studies. The implemented software, RBPSpot, scored consistently high for all the performance metrics including average accuracy of ∼90% across a large number of validated datasets. It outperformed the compared tools, including some with much complex deep-learning models, during a comprehensive benchmarking process. RBPSpot can identify RBP binding sites in the human system and can also be used to develop new models, making it a valuable resource in the area of regulatory system studies.Nitesh Kumar SharmaSagar GuptaAshwani KumarPrakash KumarUpendra Kumar PradhanRavi ShankarElsevierarticleSequence analysisSystems biologyOmicsScienceQENiScience, Vol 24, Iss 12, Pp 103381- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Sequence analysis Systems biology Omics Science Q
spellingShingle	Sequence analysis Systems biology Omics Science Q Nitesh Kumar Sharma Sagar Gupta Ashwani Kumar Prakash Kumar Upendra Kumar Pradhan Ravi Shankar RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
description	Summary: Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using an ultra-fast inexact k-mers search for statistically significant seeds. The seeds work as an anchor to evaluate the context and binding potential using flanking region information while leveraging from Deep Feed-forward Neural Network. The developed models also received support from MD-simulation studies. The implemented software, RBPSpot, scored consistently high for all the performance metrics including average accuracy of ∼90% across a large number of validated datasets. It outperformed the compared tools, including some with much complex deep-learning models, during a comprehensive benchmarking process. RBPSpot can identify RBP binding sites in the human system and can also be used to develop new models, making it a valuable resource in the area of regulatory system studies.
format	article
author	Nitesh Kumar Sharma Sagar Gupta Ashwani Kumar Prakash Kumar Upendra Kumar Pradhan Ravi Shankar
author_facet	Nitesh Kumar Sharma Sagar Gupta Ashwani Kumar Prakash Kumar Upendra Kumar Pradhan Ravi Shankar
author_sort	Nitesh Kumar Sharma
title	RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
title_short	RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
title_full	RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
title_fullStr	RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
title_full_unstemmed	RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
title_sort	rbpspot: learning on appropriate contextual information for rbp binding sites discovery
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/6f67ca246bed473b92c2e7b266e6a876
work_keys_str_mv	AT niteshkumarsharma rbpspotlearningonappropriatecontextualinformationforrbpbindingsitesdiscovery AT sagargupta rbpspotlearningonappropriatecontextualinformationforrbpbindingsitesdiscovery AT ashwanikumar rbpspotlearningonappropriatecontextualinformationforrbpbindingsitesdiscovery AT prakashkumar rbpspotlearningonappropriatecontextualinformationforrbpbindingsitesdiscovery AT upendrakumarpradhan rbpspotlearningonappropriatecontextualinformationforrbpbindingsitesdiscovery AT ravishankar rbpspotlearningonappropriatecontextualinformationforrbpbindingsitesdiscovery
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RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery

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