Abstract
BackgroundThe 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].FindingsIn 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.ConclusionOur 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.
Highlights
The H/ACA family of small nucleolar RNAs plays a central role in guiding the pseudouridylation of ribosomal RNA
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
In this report we describe some minor modifications to Fisher, a brief update on the candidate snoRNAs we reported in Edvardsson et al [1], and a comparative genome analysis using 14 available yeast genome sequences which heavily reduced the number of false positives and enabled us to identify three yeast snoRNAs not identified by Schattner and colleagues' snoGPS program
Summary
The H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In this report we describe some minor modifications to Fisher, a brief update on the candidate snoRNAs we reported in Edvardsson et al [1], and a comparative genome analysis using 14 available yeast genome sequences which heavily reduced the number of false positives and enabled us to identify three yeast snoRNAs not identified by Schattner and colleagues' snoGPS program.
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