Work

CSRDB: a small RNA integrated database and browser resource for cereals

Year: 2006

Type: article

Abstract: 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.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkl991

Authors: C. Johnson, L. Bowman, A. T. Adai, V. Vance, V. Sundaresan

Institutions: University of California, Davis, University of South Carolina, University of California, San Francisco

Language: English

Topic: Plant Molecular Biology Research

Subfield: Plant Science

Field: Agricultural and Biological Sciences

Domain: Life Sciences

SDG: Zero hunger

Open Access status: gold

Estimated APC paid: $3,992