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Nucleic Acids Research 2005 33(14):4578-4583; doi:10.1093/nar/gki754
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Published online 10 August 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database

Alexei Fedorov*, Jesse Stombaugh1, Michael W. Harr, Saihua Yu, Lorena Nasalean1 and Valery Shepelev2

Department of Medicine, Program in Bioinformatics and Proteomics/Genomics, Medical University of Ohio Toledo, OH 43614, USA 1Department of Biological Sciences, Life Sciences, Bowling Green State University Bowling Green, OH 43403, USA 2Department of Bioinformatics, Institute of Molecular Genetics, RAS Moscow 123182, Russia

*To whom correspondence should be addressed. Tel: +1 419 383 5270; Fax: +1 419 383 3102; Email: afedorov{at}meduohio.edu

Received June 3, 2005. Revised July 20, 2005. Accepted July 20, 2005.

Based on comparative genomics, we created a bioinformatic package for computer prediction of small nucleolar RNA (snoRNA) genes in mammalian introns. The core of our approach was the use of the Mammalian Orthologous Intron Database (MOID), which contains all known introns within the human, mouse and rat genomes. Introns from orthologous genes from these three species, that have the same position relative to the reading frame, are grouped in a special orthologous intron table. Our program SNO.pl searches for conserved snoRNA motifs within MOID and reports all cases when characteristic snoRNA-like structures are present in all three orthologous introns of human, mouse and rat sequences. Here we report an example of the SNO.pl usage for searching a particular pattern of conserved C/D-box snoRNA motifs (canonical C- and D-boxes and the 6 nt long terminal stem). In this computer analysis, we detected 57 triplets of snoRNA-like structures in three mammals. Among them were 15 triplets that represented known C/D-box snoRNA genes. Six triplets represented snoRNA genes that had only been partially characterized in the mouse genome. One case represented a novel snoRNA gene, and another three cases, putative snoRNAs. Our programs are publicly available and can be easily adapted and/or modified for searching any conserved motifs within mammalian introns.


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