PhD-SNPg

PhD-SNPg is a new, efficient machine learning method that is useful for quickly interpreting single nucleotide variants (SNVs) and serves as a benchmark for further tool development. This method is easy to use and only requires sequence-based features. Yet, it can still perform as well as or better than more complex methods in tackling the challenge of determining the functional effects of coding and non-coding SNVs in human genetics.

Topic

DNA polymorphism;Machine learning;Sequence assembly

Detail

  • Operation: SNP annotation;Variant calling

  • Software interface: Web user interface

  • Language: Shell;Python

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: Department of Biological, Geological, and Environmental Sciences (BiGeA) at the University of Bologna (Italy), Department of Comparative Biomedicine and Food Science, University of Padova (Italy).

  • Input: CSV,VCF,MUT

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants.
  • Capriotti E and Fariselli P. PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. 2017; 45:W247-W252. doi: 10.1093/nar/gkx369
  • https://doi.org/10.1093/nar/gkx369
  • PMID: 28482034
  • PMC: PMC5570245

Download and documentation

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