Neural computing in discovering RNA interactions

Yoshiyasu Takefuji, Dora Ben-Alon, Arieh Zaritsky

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

High-order RNA structures are involved in regulating many biological processes; various algorithms have been designed to predict them. Experimental methods to probe such structures and to decipher the results are tedious. Artificial intelligence and the neural network approach can support the process of discovering RNA structures. Secondary structures of RNA molecules are probed by autoradiographing gels, separating end-labeled fragments generated by base-specific RNases. This process is performed in both conditions, denaturing (for sequencing purposes) and native. The resultant autoradiograms are scanned using line-detection techniques to identify the fragments by comparing the lines with those obtained by 'alkaline ladders'. The identified paired bases are treated by either one of two methods to find the foldings which are consistent with the RNases' 'cutting' rules. One exploits the maximum independent set algorithm; the other, the planarization algorithm. They require, respectively, n and n2 processing elements, where n is the number of base pairs. The state of the system usually converges to the near-optimum solution within about 500 iteration steps, where each processing element implements the McCulloch-Pitts binary neuron. Our simulator, based on the proposed algorithm, discovered a new structure in a sequence of 38 bases, which is more stable than that formerly proposed.

Original languageEnglish
Pages (from-to)85-96
Number of pages12
JournalBioSystems
Volume27
Issue number2
DOIs
Publication statusPublished - 1992
Externally publishedYes

    Fingerprint

Keywords

  • Artificial intelligence
  • Biological regulation
  • High-order RNA structures
  • Maximum independent set
  • Neural nets
  • planarization algorithms

ASJC Scopus subject areas

  • Statistics and Probability
  • Modelling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Applied Mathematics

Cite this