De novo discovery of structured ncRNA motifs in genomic sequences

Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15.

Abstract

De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Computational Biology / methods*
  • Genomics / methods*
  • Nucleic Acid Conformation*
  • Nucleotide Motifs*
  • RNA, Untranslated / chemistry*
  • Sequence Analysis, RNA / methods*

Substances

  • RNA, Untranslated