General Information
| Description | A web-based platform for designing genome-specific primers in polyploids |
| Homepage | https://github.com/bioinfogenome/GSP |
Publications
GSP: a web-based platform for designing genome-specific primers in polyploids
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.
Contacts:
yong.gu@ars.usda.gov or devin.coleman-derr@ars.usda.gov
Supplementary information:
Supplementary data are available at Bioinformatics online.
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