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RPINBASE: An online toolbox to extract features for predicting RNA-protein interactions.
Torkamanian-Afshar, Mahsa; Lanjanian, Hossein; Nematzadeh, Sajjad; Tabarzad, Maryam; Najafi, Ali; Kiani, Farzad; Masoudi-Nejad, Ali.
  • Torkamanian-Afshar M; Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. Electronic a
  • Lanjanian H; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. Electronic address: h.lanjanian@ut.ac.ir.
  • Nematzadeh S; Department of Computer Technologies, Beykent University, Istanbul, Turkey. Electronic address: sajjadnematzadeh@beykent.edu.tr.
  • Tabarzad M; Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Electronic address: m_tabarzad@sbmu.ac.ir.
  • Najafi A; Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran. Electronic address: najafi74@bmsu.ac.ir.
  • Kiani F; Department of Computer Engineering, Engineering and Architecture Faculty, Istanbul Arel University, Istanbul, Turkey.
  • Masoudi-Nejad A; Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. Electronic a
Genomics ; 112(3): 2623-2632, 2020 05.
Article in English | MEDLINE | ID: covidwho-1478
ABSTRACT
Feature extraction is one of the most important preprocessing steps in predicting the interactions between RNAs and proteins by applying machine learning approaches. Despite many efforts in this area, still, no suitable structural feature extraction tool has been designed. Therefore, an online toolbox, named RPINBASE which can be applied to different scopes of biological applications, is introduced in this paper. This toolbox employs efficient nested queries that enhance the speed of the requests and produces desired features in the form of positive and negative samples. To show the capabilities of the proposed toolbox, the developed toolbox was investigated in the aptamer design problem, and the obtained results are discussed. RPINBASE is an online toolbox and is accessible at http//rpinbase.com.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / RNA / RNA-Binding Proteins Type of study: Prognostic study Language: English Journal: Genomics Journal subject: Genetics Year: 2020 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / RNA / RNA-Binding Proteins Type of study: Prognostic study Language: English Journal: Genomics Journal subject: Genetics Year: 2020 Document Type: Article