Can anyone suggest a freely available software to detect synonymous and nonsynonymous SNPs within a gene?

All Answers (9) Show full discussion

• 
  Paula Moreno Sanz · Istituto Agrario di San Michele all’Adige (IASMA), Fondazione Edmund Mach

  Yes, it does

  Cancel Save

  Yes, it does

  Jul 6, 2012
• 
  Bharati Mehani · Institute of Genomics and Integrative Biology

  U can go for PLINK too

  Cancel Save

  U can go for PLINK too

  Jul 9, 2012
• 
  Saeid Ghorbian · Islamic Azad University

  Yes, it does

  Cancel Save

  Yes, it does

  Jul 9, 2012
• 
  Yujun Cui · Beijing Institute of Microbiology and Epidemiology

  DNAsp is a suitable tool if you have only a few pieces of sequences. But if you want to perform the analysis on a large batch of data, like several hundreds of genes, some tools based on Linux would help.

  Cancel Save

  DNAsp is a suitable tool if you have only a few pieces of sequences. But if you want to perform the analysis on a large batch of data, like several hundreds of genes, some tools based on Linux would help.

  Jul 12, 2012
• 
  Patrick Sulem · deCODE genetics, Inc.

  Variant effect predictor from Ensembl, it does have a web based access. It includes HGVS and HGNC. Official nomenclature for variant and genes. Good luck . LEt me know how you find it.

  Cancel Save

  Variant effect predictor from Ensembl, it does have a web based access. It includes HGVS and HGNC. Official nomenclature for variant and genes.
  Good luck . LEt me know how you find it.

  Aug 19, 2012
• 
  Patrick Sulem · deCODE genetics, Inc.

  http://www.ensembl.org/info/docs/variation/vep/index.html VEP

  Cancel Save

  http://www.ensembl.org/info/docs/variation/vep/index.html
  VEP

  Aug 19, 2012
• 
  Isabelle Creveaux · Centre Hospitalier Universitaire de Clermont-Ferrand

  You may use on the web site Mutalyzer the variant description extractor (https://mutalyzer.nl/descriptionExtract). It will allow you to compare your observe sequence with the reference sequence. It will include variant description with HGVS nomenclature.

  Cancel Save

  You may use on the web site Mutalyzer the variant description extractor (https://mutalyzer.nl/descriptionExtract). It will allow you to compare your observe sequence with the reference sequence. It will include variant description with HGVS nomenclature.

  Sep 12, 2012
• 
  Barbara Fussi · Bayerisches Amt für forstliche Saat- und Pflanzenzucht

  Variant effect predictor from Ensembl does not include any plant species, so I cannot use it :( but thanks for your suggestion.

  Cancel Save

  Variant effect predictor from Ensembl does not include any plant species, so I cannot use it :( but thanks for your suggestion.

  Sep 25, 2012