Nucleic Acids Research Advance Access published online on September 20, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl672
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome
Key Laboratory of Gene Engineering of the Ministry of Education, Zhongshan University Guangzhou 510275, PR China 1 State Key Laboratory for Biocontrol, Zhongshan University Guangzhou 510275, PR China
*To whom correspondence should be addressed at Biotechnology Research Center, Zhongshan University, Guangzhou 510275, PR China. Tel: +86 20 84112399; Fax: +86 20 84036551; Email: lsbrc16{at}zsu.edu.cn
Received August 28, 2006. Accepted August 29, 2006.
Small nucleolar RNAs (snoRNAs) represent an abundant group of non-coding RNAs in eukaryotes. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Current snoRNA-searching programs, which are essentially based on sequence complementarity to rRNAs or snRNAs, exist only for the screening of guide snoRNAs. In this study, we have developed an advanced computational package, snoSeeker, which includes CDseeker and ACAseeker programs, for the highly efficient and specific screening of both guide and orphan snoRNA genes in mammalian genomes. By using these programs, we have systematically scanned four human–mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern. The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.
*Correspondence may also be addressed to Liang-Hu Qu. Tel/Fax: +86 20 84112399; Email: lsbrc04{at}zsu.edu.cn
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