Homology searches for structural RNAs: from proof of principle to practical use
- Janelia Research Campus, Ashburn, Virginia 20147, USA
- Corresponding author: sean{at}eddylab.org
This extract was created in the absence of an abstract.
If you search a sequence database for homologs of a structural RNA, you don't want to search just for linear sequence similarity; you also want the search program to consider whether a candidate sequence can be folded into a similar base-paired secondary structure. A powerful and general class of computational methods for combining primary sequence and secondary structure information in RNA homology searches was independently introduced just over 20 years ago by Yasu Sakakibara (working in the lab of David Haussler) and by myself (working as a postdoc with Richard Durbin). The 20th anniversary of the founding of the RNA journal seems a good occasion to look back at the 20 year development arc of “stochastic context-free grammar” (SCFG) methods and software for structural RNA homology searches.
My interest in RNA sequence analysis started when I was working on the three catalytic group I introns in bacteriophage T4. The T4 …
