title: GSP: a web-based platform for designing genome-specific primers in polyploids.
abstract: The sequences among subgenomes in a polyploid species have high similarity, making it difficult to design genome-specific primers for sequence analysis.
  
  
  
  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.
  
  
  
  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 data are available at Bioinformatics online.
authors.affiliation: USDA-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.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
authors.forename: Vijay K
authors.initials: VK
authors.lastname: Tiwari
authors.affiliation: Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
authors.forename: Nidhi
authors.initials: N
authors.lastname: Rawat
authors.affiliation: Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
authors.forename: Bikram S
authors.initials: BS
authors.lastname: Gill
authors.affiliation: USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.
authors.forename: Naxin
authors.initials: N
authors.lastname: Huo
authors.affiliation: Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
authors.forename: Frank M
authors.initials: FM
authors.lastname: You
authors.affiliation: USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
authors.forename: Devin
authors.initials: D
authors.lastname: Coleman-Derr
authors.affiliation: USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
mesh_terms: D017931:DNA Primers; D020407:Internet; D011123:Polyploidy; D016415:Sequence Alignment; D012984:Software
chemical_list: D017931:DNA Primers