A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.
BACKGROUND
Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date.


RESULTS
We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.
Edvardsson
Sverker
S
Department of Information Technology, Mid Sweden University, S-851 70, Sundsvall, Sweden.
Gardner
Paul P
PP
Poole
Anthony M
AM
Hendy
Michael D
MD
Penny
David
D
Moulton
Vincent
V
D000465:Algorithms; D001483:Base Sequence; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D004735:Energy Transfer; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020537:RNA, Small Nucleolar / Q000032:analysis / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
D020537:RNA, Small Nucleolar