De novo discovery of structured ncRNA motifs in genomic sequences

Walter L Ruzzo; Jan Gorodkin

doi:10.1007/978-1-62703-709-9_15

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.

Authors

Walter L Ruzzo¹, Jan Gorodkin

Affiliation

¹ Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.

PMID: 24639166
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