Arabidopsis SNP-At Browser Help

 

    The Arabidopsis non-synonymous single nucleotide polymorphism (SNP-At) browser provides a simple way to browse changes to coding regions caused by SNPs in accessions or natural variants of Arabidopsis.
 
Arabidosis SNP Data
The data underlying SNP-At is obtained from the Arabidopsis 1001 Genomes Project as processed SNP calls. We have created a pipeline to take these processed data and constructs pseudo chromosomes for each accession based on the Arabidopsis accession Col-0 genome sequence obtained from TAIR (currently TAIR9). From these pseudo chromosomes for each accession, we extract and compile proteins sets which are compared to the reference protein from TAIR.
 
Using At nsSNP
SNP-At browser

The data for a given AGI can be retrieved by entering the code into the window on the top left and clicking the "Retrieve" button. The current description for the protein is displayed (TAIR9) with the protein represented as a bar scale with numbers indicating amino acid number. The red/grey spheres indicate a nsSNP or amino acid substitution has occurred at this point along the protein with the top track representing a consolidation or summary of all nsSNPs in the protein. The letter in the red/grey sphere corresponds to the substituted amino acid (1 letter code) as a result of the nsSNP. The size of the red/grey sphere indicates the number of accessions or natural variants that have contributed to a specific nsSNP or substitution. The larger the red/grey sphere the more accessions have contributed to the change.
By employing (mouse click) the triangle in the dark grey "Control Box" a list of Arabidopsis accessions that contain nsSNPs to the particular protein are displayed.
 
The specific nsSNP from each Arabidopsis accession can be viewed by toggling the "+" symbol next to the accession name / code. In this instance Bur-0 has contributed one change and Bur-0 has contributed one change.
 

By panning the bar scale (protein) with the mouse (grab and pan) and employing the mouse wheel to zoom, the specific substitutions can be observed. In this example Bur-0 has a SNP that causes a substitution at Met (106), resulting in an Ile; while Ped-0 contains a SNP that causes Thr at position 141 to be substituted with a Ser.