title: Using temperature effects to predict the interactions between two RNAs.
abstract: BACKGROUND
  Interaction of two RNA molecules is considered as an important factor that regulates gene expression post-transcriptional process. Most of the ncRNAs prevent the translation of their target mRNA(s) by forming stable bindings with them. Although several computational methods have been proposed to predict the interactions between two RNAs, none of them can produce reliable and accurate results.
  
  
  RESULTS
  In this paper, a new approach entitled tempRNAs is presented to accurately predict interaction structure between two RNAs based on a gradual temperature decrease. For each specified temperature, our algorithm contains two main steps. First, the secondary structure of each RNA is determined with respect to the previous base pairs as constraints. Second, two RNAs are concatenated and then the interaction between them is calculated according to the previous base pairs. The secondary structures are determined based on minimum free energy model. The proposed algorithm is evaluated for a set of known interacting RNA pairs. The results show the higher accuracy of the proposed method in comparison to the other state-of-the-art algorithms, namely inRNAs and RactIP.
authors.affiliation: Department of Computer Science, School of Mathematics, Statistics, and Computer Science, University of Tehran, Tehran, Iran. Electronic address: mgtabesh@ut.ac.ir.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Ganjtabesh
authors.affiliation: Department of Computer Science, School of Mathematics, Statistics, and Computer Science, University of Tehran, Tehran, Iran. Electronic address: s.montaseri@ut.ac.ir.
authors.forename: Soheila
authors.initials: S
authors.lastname: Montaseri
authors.affiliation: Department of Computer Science, Faculty of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran. Electronic address: f.zare@aut.ac.ir.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Zare-Mirakabad
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000378:metabolism; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry*; D013696:Temperature
chemical_list: D012329:RNA, Bacterial
keywords: Minimum free energy; RNA secondary structure; RNA–RNA interaction