Title: TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes

Authors: Leilei Guo, Dong Zhang, Yingfeng Wang, Russell L. Malmberg, Michael J. McEachern, Liming Cai

Addresses: Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA. ' Plant Genome Mapping Lab, University of Georgia, 0240 CAGT, 111 Riverbend Rd., Athens, GA 30602, USA. ' Department of Computer Science, University of Georgia, 0415 Boyd Grad Rsch Ctr, 200 D.W. Brooks Dr., Athens, GA 30602, USA. ' Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences Building, Athens, GA 30602-7271, USA. ' Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA. ' Department of Computer Science, University of Georgia, 0415 Boyd Grad Rsch Ctr, 200 D.W. Brooks Dr., Athens, GA 30602, USA

Abstract: The identification of Telomerase RNAs (TRs) has been difficult owing to their rapid evolutionary divergence. The common core structure found in all known TRs contains a pseudoknot and a triple helix, which are beyond the capability of existing RNA-structure-profiling techniques. We describe a novel approach to predict the structure of key TR features and to aid the identification of TRs in genomes, using a program we developed, TRFolder. We applied our method to confirm and improve previously studied core structures from Saccharomyces and Kluyveromyces TRs. We made novel structural predictions of core elements of the TRs from Schizosaccharomyces pombe, Candida albicans, and several other yeast species.

Keywords: yeast telomerase RNA; RNA pseudoknot; RNA secondary structure prediction; telomerase RNA core structure; telomeric template; pairwise complementary alignment; yeast genomes; bioinformatics.

DOI: 10.1504/IJBRA.2011.039170

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.1, pp.63 - 81

Received: 26 Apr 2010
Accepted: 07 Jun 2010
Published online: 24 Jan 2015 *

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