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Bioinformatics. 2016 Aug 1;32(15):2382-3. doi: 10.1093/bioinformatics/btw134. Epub 2016 Mar 9.

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

Author information

  • 1USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
  • 2Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
  • 3USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.
  • 4Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
  • 5USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.

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.

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.

PMID:
27153733
DOI:
10.1093/bioinformatics/btw134
[PubMed - in process]
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