Genome-Specific Primers in Polyploid Species

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The sequences among subgenomes in a polyploid species share high similarity. This makes it difficult to design genome-specific primers for sequence analysis. GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in the polyploid wheat genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in the existing databases, performs a multiple sequence alignment, and designs primers based on sequence variants in the alignment. An interactive primer diagram, a sequence alignment viewer, and a virtual electrophoresis images are displayed as parts of the primer design results. GSP also designs specific primers from multiple sequences uploaded by users. GSP is a user-friendly and efficient web platform freely available at http://probes.pw.usda.gov/GSP

A manuscript is in preparation by Wang et al. entitled: "GSP: a web-based tool for designing genome-specific primers in wheat." For more information, contact Yi Wang (Yi.Wang@ars.usda.gov).