Bioinformatics Advance Access originally published online on July 9, 2004
Bioinformatics 2004 20(18):3293-3301; doi:10.1093/bioinformatics/bth394
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.
Discovery Note |
A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome
1 Department of Genetics, General and Molecular Biology, University of Naples ‘Federico II’, via Mezzocannone 8, 80134 Napoli, Italy, 2 Institute of Genetics and Biophisics Adriano Buzzato Traverso, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy and 3 Department of Clinical and Biological Sciences, University of Torino, Regione Gonzole 10, 10043 Orbassano (TO), Italy
Received on December 23, 2003; revised on May 9, 2003; accepted on June 26, 2004
Advance Access Publication July 9, 2004
Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome.
Results: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules.
Availability: Additional information is available at http://www.bioinformatica.unito.it/bioinformatics/snoRNAs
Contact: raffaele.calogero{at}unito.it
* To whom correspondence should be addressed.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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