Journal of Proteomics & Bioinformatics

Journal of Proteomics & Bioinformatics
Open Access

ISSN: 0974-276X

+44 1223 790975

Yong-Bi Fu

Yong-Bi Fu
Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada,
107 Science Place, Saskatoon, SK S7N 0X2

  • Research Article
    paSNPg: A GBS-Based Pipeline for Protein-Associated SNP Discovery and Genotyping in Non-Model Species
    Author(s): Yong-Bi Fu and Yibo DongYong-Bi Fu and Yibo Dong

    Genotyping-by-sequencing (GBS) has recently developed as a feasible genomic approach for exploring genome-wide genetic variation for population and evolutionary genomic analyses of non-model species. To facilitate the acquisition of function-associated genetic variation data in natural populations, we present a GBS-based pipeline called paSNPg for protein-associated SNP (paSNP) discovery and genotyping in non-model organisms. The pipeline was developed through the expansion of the published npGeno utility to assemble nuclear contigs from raw GBS sequence data, separate protein-associated contigs from all assembled contigs based on published PEP (or Predictions on Entire Proteomes) sequence data sets, and call paSNPs across assayed samples based on protein-associated contigs. Testing the pipeline with two GBS sequence data sets, Arabidopsis thaliana and Oryza sativa, revealed its poten.. View More»
    DOI: 10.4172/jpb.1000368

    Abstract PDF

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