GSP: a web-based platform for designing genome-specific primers in polyploids.

Wang, Y., Tiwari, V.K., Rawat, N., Gill, B.S., Huo, N., You, F.M., Coleman-Derr, D., and Gu, Y.Q. (2016). "GSP: a web-based platform for designing genome-specific primers in polyploids.", Bioinformatics, 32(6), pp. 1-2. doi : 10.1093/bioinformatics/btw134  Access to full text

Abstract

Motivation: The sequences among subgenomes in a polyploid species have high similarity, making it difficult to design genome-specific primers for sequence analysis. Results: We present GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in existing databases, performs a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primers diagram, a sequence alignment viewer, and a virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users.

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