New features in Allelle Search Tool
New features include selecting specific strains and multiple output displays.
The Allele Search Tool returns alleles from markers in a chosen diversity collection from a region or around a gene.
Select a variant collection
- Mutiple different genotype studies available, including genotype studies US soybean germplasm collection using the SoySNP50K BeadChip
Select strain analysis type and Select genotype display
- Clicking on ‘All strains’ radio button, all strains will be searched
- By clicking on ‘Specific strain’ radio button the lists of strains appears
- The filter text box allows you to search for a particular strain
- Highlight the strain or stains you want to search
Select genotype display
- The HapMap display reports the specific observed nucleotides (e.g., A, G)
- The VCF display reports data as reference-relative states (0/1)
Search by Identifier
- Enter a gene identifier and flanking regions or select by genomic region by selecting a chromosome and start and stop coordinates
The tool will return the selected strains with position and allele status of any SNPs in the requested region. This information is important to assays of gene functional differences and to the design of markers for further analysis.