Artificial Life and Robotics

, Volume 19, Issue 2, pp 209–214 | Cite as

A detection method for snoRNA modification domain by fully indexable dictionary retrieving

  • Takayuki Yamamoto
  • Kunihito Yamamori
  • Naoya Kenmochi
  • Masaru Aikawa
Original Article
  • 81 Downloads

Abstract

Recently, non-coding RNA which participates with organic activities has been found in non-coding region. Until now, we do not know detailed function of non-coding RNAs very well. To make clear functions of non-coding RNAs, we need to obtain a lot of data about non-coding RNAs and their targets. However, we do not have efficient techniques to analyze relations between non-coding RNAs and their targets. In this paper, we propose a high-speed method that can detect modification domain candidates on the target RNA based on the small nucleolar RNA (snoRNA) sequence. A snoRNA modifies a target RNA by composing complementary base pairs between a part of snoRNA and a part of target RNA. Our method stores the relations between snoRNA sequences and their target in a Fully Indexable Dictionary built by Trie data structure and Level-Order Unary Degree Sequence for high-speed retrieving.

Keywords

LOUDS rRNA snoRNA Succinct data structure Trie 

References

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Copyright information

© ISAROB 2014

Authors and Affiliations

  • Takayuki Yamamoto
    • 1
  • Kunihito Yamamori
    • 1
  • Naoya Kenmochi
    • 1
  • Masaru Aikawa
    • 1
  1. 1.Faculty of Engineering, University of MiyazakiMiyazakiJapan

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