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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., Gu, Y.Q. (2016). GSP: A web-based platform for designing genome-specific primers in polyploids, 32(15), 2382-2383. http://dx.doi.org/10.1093/bioinformatics/btw134

Abstract

© 2016 The Author 2016. Published by Oxford University Press. All rights reserved. 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. Availability and implementation: GSP is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/GSP. Source code and command-line application are available at https://github.com/bioinfogenome/GSP.

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