Nucleic Acids Research Advance Access first published online on September 20, 2006
This version published online on October 6, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl672
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
© 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 July 6, 2006. Revised August 28, 2006. Accepted August 28, 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
The history dates have been corrected.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. P. Hoeppner, S. White, D. C. Jeffares, and A. M. Poole Evolutionarily Stable Association of Intronic snoRNAs and microRNAs with Their Host Genes Gen Biol Evol, November 23, 2009; 2009(0): 420 - 428. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Solda, I. V. Makunin, O. U. Sezerman, A. Corradin, G. Corti, and A. Guffanti An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes Brief Bioinform, September 1, 2009; 10(5): 475 - 489. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H.-M. Chen and S.-H. Wu Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis Nucleic Acids Res., May 1, 2009; 37(9): e69 - e69. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Morita, Y. Saito, K. Sato, K. Oka, K. Hotta, and Y. Sakakibara Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans Nucleic Acids Res., February 1, 2009; 37(3): 999 - 1009. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Hertel, I. L. Hofacker, and P. F. Stadler SnoReport: computational identification of snoRNAs with unknown targets Bioinformatics, January 15, 2008; 24(2): 158 - 164. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Piekna-Przybylska, W. A. Decatur, and M. J. Fournier The 3D rRNA modification maps database: with interactive tools for ribosome analysis Nucleic Acids Res., January 11, 2008; 36(suppl_1): D178 - D183. [Abstract] [Full Text] [PDF]
|
|