Nucleic Acids Research Advance Access originally published online on November 11, 2006
Nucleic Acids Research 2007 35(Database issue):D183-D187; doi:10.1093/nar/gkl873
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Nucleic Acids Research, 2007, Vol. 35, Database issue D183-D187
Published by Oxford University Press 2006
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.
Articles |
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs
State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University 220 Handan Road, 200433 Shanghai, China 1 Deptartment of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen 37077 Goettingen, Germany 2 Center for Genomics and Bioinformatics, Karolinska Institute Berzelius Väg 35, 17177 Stockholm, Sweden
*To whom correspondence should be addressed. Tel: +86 21 5566 4556; Fax: +86 21 5566 4556; Email: xiejun{at}fudan.edu.cn
Received August 15, 2006. Revised October 4, 2006. Accepted October 5, 2006.
Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.
*Correspondence may also be addressed to Weilin Wu. Tel: +46 8 5248 7396; Fax: +46 8 323672; Email: Weilin.Wu{at}cgb.ki.se
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