A Structure-Based Flexible Search Method for Motifs in RNA

The discovery of non-coding RNA (ncRNA) motifs and their role in regulating gene expression has recently attracted considerable attention. The goal is to discover these motifs in a sequence database. Current RNA motif search methods start from the primary sequence and only then take into account secondary structure considerations. One can think of developing a flexible structure-based motif search method that will filter datasets based on secondary structure first, while allowing extensive primary sequence factors and additional factors such as potential pseudoknots as constraints. Since different motifs vary in structure rigidity and in local sequence constraints, there is a need for algorithms and tools that can be fine-tuned according to the searched RNA motif, but differ in their approach from the RNAMotif descriptor language. We present an RNA motif search tool called STRMS (Structural RNA Motif Search), which takes as input the secondary structure of the query, including loc...

• Type: Journal
• Year: 2007
• Where: JCB
• Authors: Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem
• Keywords: JCB 2007, Primary Sequence, RNA Motifs, Secondary Structure