Journal article

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction

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Publication Details

Author list: Edvardsson, Sverker;Moulton, Vincent

Publication year: 2003

Start page: 865

End page: 873

Number of pages: 9

ISSN: 1367-4803

DOI: http://dx.doi.org/10.1093/bioinformatics/btg080

View additional information: View in Web of Science


Abstract

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.


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