Bioinformatics Vol. 19 no. 7 2003
Pages 865-873
© 2003 Oxford University Press
A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction
1 Department of Information Technology, Mid
Sweden University, S-851 70, Sundsvall, Sweden
2 Institute of Fundamental Science
3 Institute of Molecular BioScience
4 Allan Wilson Centre for Molecular Ecology
and Evolution, Massey University, Palmerston North, New Zealand
6 The Linnaeus Centre for Bioinformatics,
Uppsala University, BMC Box 598, S-751 24, Uppsala, Sweden
Received on June 7, 2002
; revised on November 1, 2002
; accepted on November 26, 2002
Motivation: 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.
Contact: vincent.moulton{at}lcb.uu.se
Supplementary Information: Tables 1–5 referred to in the text can be downloaded from http://RNA.massey.ac.nz/fisher/
* To whom correspondence should be addressed.
Both authors contributed equally
to this work.
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