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PolyMarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid organisms. PolyMarker generates a multiple alignment between the target SNP sequence and the chromosome survey sequences. It then generates a mask with informative positions which are highlighted with respect to the target genome. Because many users are analysing the wheat genome this is provided and doesn't need to be uploaded.
Test data for this app are available in the Discovery Environment under >Shared with me>rosysnake>example_polymarker.
The input file must be uploaded as a CSV file with the following columns:
- Gene id: An unique identifier for the assay. It must be unique on each run.
- Target chromosome: In the form 1A, 2D, 7B, etc…
- Sequence: The sequence flanking the SNP. The SNP must be marked in the format [A/T] for a varietal SNP with alternative bases, A or T.
If the user wish to analyse an organism different from wheat (or wish to use another version of its genome) a reference FASTA file is also needed.
Parameters Used in App
There are no required parameters, the app can be run with the default settings. For a list of possible options see the link at the bottom of the page.
The mask contains the details of the local alignment. Multiple intermediate files will also be available.