AutoSNPdb
QFAB have worked in collaboration with Australian Centre for Plant Functional Genomics (ACPFG) to develop an integrated SNP discovery pipeline and a custom relational database for the important crops of rice, barley and brassica.
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.
How it works
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 by way of a user-friendly graphical interface.
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Omics Research Case Studies