Nucleic Acids Research Advance Access originally published online on December 14, 2006
Nucleic Acids Research 2007 35(Database issue):D829-D833; doi:10.1093/nar/gkl991
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Nucleic Acids Research, 2007, Vol. 35, Database issue D829-D833
© 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.
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CSRDB: a small RNA integrated database and browser resource for cereals
1 Section of Plant Biology, College of Biological Sciences, University of California Davis, CA 95616, USA 2 Department of Biological Sciences, University of South Carolina Columbia, SC 29208, USA 3 Biological and Medical Informatics, University of California San Francisco, CA 94143, USA 4 Department of Plant Sciences, College of Agricultural Sciences, University of California Davis, CA 95616, USA
*To whom correspondence should be addressed. Tel: +1 530 754 9852; Fax: +1 530 752 5410; Email: camjohnson{at}ucdavis.edu
Received August 15, 2006. Revised October 26, 2006. Accepted October 30, 2006.
Plant small RNAs (smRNAs), which include microRNAs (miRNAs), short interfering RNAs (siRNAs) and trans-acting siRNAs (ta-siRNAs), are emerging as significant components of epigenetic processes and of gene networks involved in development and in homeostasis. Here we present a bioinformatics resource for cereal crops, the Cereal Small RNA Database (CSRDB), consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing. The smRNA sequences have been mapped to the rice genome and to the available maize genome sequence and these results are presented in two genome browser datasets using the Generic Genome Browser. Potential RNA targets for the smRNAs have been predicted and access to the resulting smRNA/RNA target pair dataset has been made available through a MySQL based relational database. Various ways to access the data are provided including links from the genome browser to the target database. Data linking and integration are the main focus for this interface, and internal as well as external links are present. The resource is available at http://sundarlab.ucdavis.edu/smrnas/ and will be updated as more sequences become available.
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