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Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics -- assessment and update.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, The Linnaeus Centre for Bioinformatics.
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2008 (English)In: BMC Research Notes 2008, Vol. 1, no 49Article in journal (Other (popular scientific, debate etc.)) Published
Abstract [en]

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.

Conclusions

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.

Place, publisher, year, edition, pages
2008. Vol. 1, no 49
Identifiers
URN: urn:nbn:se:uu:diva-17626OAI: oai:DiVA.org:uu-17626DiVA: diva2:45397
Available from: 2008-07-29 Created: 2008-07-29 Last updated: 2011-01-11

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