Genome-Wide Search for Pseudoknotted Noncoding RNA: A Comparative Study

Meghana Vasavada, Kevin Byron, Yang Song, Jason T.L. Wang

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations


Noncoding RNAs (ncRNAs) are functional RNA molecules, which are involved in many biological processes including gene regulation, chromosome replication, and RNA modification. There are two tools, RNA via tree decomposition (RNATOPS) and inference of RNA alignment (Infernal), which are capable of performing genome-wide pseudoknotted ncRNA search. This chapter conducts a comparative study on RNATOPS and Infernal. It analyzes and compares the performances of the two tools with respect to their ncRNA detection accuracies. The chapter presents some background materials related to this study. It describes the methodology used in the analysis of pseudoknotted ncRNA search, and also presents some experimental results and an interpretation of these results. It was observed that RNATOPS detected ncRNAs with less computation time than Infernal due to the filter functions incorporated in the RNATOPS tool. On the other hand, Infernal yields more hits than RNATOPS.

Original languageEnglish (US)
Title of host publicationPattern Recognition in Computational Molecular Biology
Subtitle of host publicationTechniques and Approaches
Number of pages10
ISBN (Electronic)9781119078845
ISBN (Print)9781118893685
StatePublished - Dec 28 2015
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Engineering


  • Biological processes
  • Genome-wide pseudoknotted ncRNA search
  • Inference of RNA alignment
  • RNA via tree decomposition


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