Yi Wang1, Vijay K Tiwari2, Nidhi Rawat2, Bikram S Gill2, Naxin Huo3, Frank M You4, Devin Coleman-Derr5, Yong Q Gu3. 1. 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. 2. Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA. 3. USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA. 4. Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada. 5. USDA-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.
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.
Authors: Victoria C Blake; Margaret R Woodhouse; Gerard R Lazo; Sarah G Odell; Charlene P Wight; Nicholas A Tinker; Yi Wang; Yong Q Gu; Clay L Birkett; Jean-Luc Jannink; Dave E Matthews; David L Hane; Steve L Michel; Eric Yao; Taner Z Sen Journal: Database (Oxford) Date: 2019-01-01 Impact factor: 3.451
Authors: Alexander Mahlandt; Nidhi Rawat; Jeff Leonard; Prakash Venglat; Raju Datla; Nathan Meier; Bikram S Gill; Oscar Riera-Lizarazu; Gary Coleman; Angus S Murphy; Vijay K Tiwari Journal: Theor Appl Genet Date: 2021-04-08 Impact factor: 5.574