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Open Access Technical Note

Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics – assessment and update

Eva Freyhult16, Sverker Edvardsson2, Ivica Tamas37, Vincent Moulton4 and Anthony M Poole35*

Author Affiliations

1 The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, S-751 24 Uppsala, Sweden

2 Department of Natural Sciences, Mid Sweden University, S-851 70, Sundsvall, Sweden

3 Department of Molecular Biology & Functional Genomics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden

4 School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

5 School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand

6 Department of Clinical Microbiology, Clinical Bacteriology, Umeå University, 901 85 Umeå, Sweden

7 Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada

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BMC Research Notes 2008, 1:49  doi:10.1186/1756-0500-1-49

Published: 21 July 2008

Abstract

Background

The H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program – Fisher – and previously presented several candidate snoRNAs based on our analysis [1].

Findings

In this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs [2] identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in [1], and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program [3]. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material.

Conclusion

Our results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.