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Nucleic Acids Res. 2009 Jan;37(Database issue):D951-3. doi: 10.1093/nar/gkn650. Epub 2008 Oct 14.

AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants.

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1
Australian Centre for Plant Functional Genomics, Brisbane, School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.

Abstract

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/.

PMID:
18854357
PMCID:
PMC2686484
DOI:
10.1093/nar/gkn650
[Indexed for MEDLINE]
Free PMC Article
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