Shape based indexing for faster search of RNA family databases

Background: Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally annotated RNA families. Unfortunately, searching for new family members using covariance models (CMs) is very time consuming. Filtering approaches that use the sequence conservation to reduce the number of CM searches, are fast, but it is unknown to which sacrifice. Results: We present a new filtering approach, which exploits the family specific secondary structure and significantly reduces the number of CM searches. The filter eliminates approximately 85% of the queries and discards only 2.6% true positives when evaluating Rfam against itself. First results also capture previously undetected non-coding RNAs in a recent human RNAz screen. Conclusion: The RNA shape index filter (RNAsifter) is based on the following rationale: An RNA family is characterised by structure, much more succinctly than by sequence co...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Stefan Janssen, Jens Reeder, Robert Giegerich
• Keywords: BMCBI 2008, Rfam Data Base, RNA Families, Secondary Structures