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SNiPlay

SNiPlay

Web-based tool, polymorphism discovery and analysis. 1. A pipeline combining tools to detect SNPs and to compute statistical indices and graphical layouts for SNP data. It sends sequences and genotyping data into a series of modules; physical mapping to a reference genome, annotation, SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D). 2. A database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects.

Topic

Biology, Genetics

Details

  • Operation: Sequence analysis, Sequence visualisation, Genetic variation analysis, SNP detection
  • Software interface: Web user interface
  • Language: Perl
  • License: Not stated
  • Cost: Free
  • Version name: 3.0
  • Credit: Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.
  • Contact: -
  • Collection: -

Publications

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P "SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects." BMC Bioinformatics 2011 https://doi.org/10.1186/1471-2105-12-134
PMID: 21545712
PMCID: PMC3102043


Download and documentation




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