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Nucleic Acids Research Advance Access published online on October 14, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn650
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© 2008 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.

Database Issue

AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants

Chris Duran1,2, Nikki Appleby1,2, Terry Clark1,2, David Wood1,3, Michael Imelfort1,2, Jacqueline Batley1,4 and David Edwards1,2,*

1Australian Centre for Plant Functional Genomics, Brisbane, School of Land, Crop and Food Sciences, 2The Institute for Molecular Bioscience, 3Queensland Facility for Advanced Bioinformatics, The Institute for Molecular Bioscience, ARC Centre of Excellence in Bioinformatics and 4ARC Centre of Excellence for Integrative Legume Research, University of Queensland, Brisbane, QLD 4072, Australia

*To whom correspondence should be addressed. Tel: +61 (0)7 3346 2615; Fax: +61 (0)7 3346 2101; Email: Dave.Edwards{at}uq.edu.au

Received August 12, 2008. Revised September 15, 2008. Accepted September 18, 2008.

Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic marker as they represent the finest resolution of a DNA sequence (a single nucleotide), are generally abundant in populations and have a low mutation rate. Analysis of assembled EST sequence data provides a cost-effective means to identify large numbers of SNPs associated with functional genes. We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The database is freely accessible at http://autosnpdb.qfab.org.au/.


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