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Sno/scaRNAbase


NAR Molecular Biology Database Collection entry number 962
Xie J.1, Zhang M.2, Zhou T.1, Hua X.1, Tang L.S.1 and Wu W.L.3
1State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 200433 Shanghai, China
2Dept. of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077 Goettingen, Germany
3Center for Genomics and Bioinformatics, Karolinska Institute, 17177 Stockholm, Sweden

Database Description

Sno/scaRNA database (sno/scaRNAbase, http://bioinfo.fudan.edu.cn/snoRNAbase.nsf) was developed to facilitate the research of small nucleolar RNAs (snoRNAs) and cajal body-specific RNAs (scaRNAs) that have been found to play important roles in rRNA, tRNA, snRNA and even mRNA biogenesis. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase currently contains 1,979 sno/scaRNAs records obtained from 85 organisms. It provides an easy-to-use gateway to important sno/scaRNAs features such as conserved sequence motifs and antisense elements of sno/scaRNA families, methylation or pseudouridylationsites that a sno/scaRNA guides, homologues, predicted secondary structures, genomics organizations, sno/scaRNA genes, chromosome locations, functions that are experimentally verified or predicted, etc. 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. This sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research.

Acknowledgements

This research is funded by Shanghai R&D Public Service Platform and Natural Science Foundations of China (No. 30300059, 30470356).

References

1. Xie J, Zhang M, Zhou T, Hua X, Tang LS, and Wu WL. (2007) Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. Nucleic Acids Res. (2007) 35: in press.


Go to the abstract in the NAR 2007 Database Issue.
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