A SIMPLE METHOD FOR FINDING STRUCTURALLY SIMILAR RNAS USING TWO-DIMENSIONAL DISCRETE CONVOLUTION Conference Paper uri icon

abstract

  • As many noncoding RNA (ncRNA) families have well-conserved secondary structures, it is important to consider structural similarity when searching for RNA homologues. However, algorithms for detecting structural similarity tend to have high computational costs, making them unsuitable for large-scale genome screening. In this paper, we introduce a simple method that can find structurally similar RNAs at a low computational cost. The method uses matched filtering of base-pair matrices to identify structurally similar RNAs in a given database. As the matched filtering involves a simple two-dimensional discrete convolution, it has a relatively low complexity of O(L2N) for any kind of RNA secondary structure, where L is the length of the target RNA and N is the number of base-pairs in the reference RNA. 2008 IEEE.

name of conference

  • 2008 IEEE International Workshop on Genomic Signal Processing and Statistics

published proceedings

  • 2008 IEEE International Workshop on Genomic Signal Processing and Statistics

author list (cited authors)

  • Yoon, B.

citation count

  • 0

complete list of authors

  • Yoon, Byung-Jun

publication date

  • January 2008