varSEAK Online - GLOBAL varSEAK DATABASE
AND SPLICE SITE PREDICTION

Watch our tutorial for the new Splice Site Prediction Tool!

varSEAK Online

varSEAK Online – available at www.varSEAK.bio – is the publicly accessible part of the varSEAK database, including our splice site prediction tool, now available in version 2.0. Browse varSEAK Online to view variants, classifications and summarized information from the varSEAK global database as well as public databases.


varSEAK Online is completely free of charge - try it now!

Use the Splice Site Prediction Tool to check variants for a potential effect on splicing. By automatically comparing all potential splice sites surrounding the variant, the tool can predict whether and which other splice site is the most likely to be used with an accuracy of over 96%.

If you would like to include JSI's SSP 2.0 in your analysis pipeline, a precompiled C library is available upon request, which can be integrated into most pipelines.

  • HIGHLIGHTS

    • Search for a gene and find all variants of a gene in one clearly organized table, including:
      • hg19 and hg38 positions
      • HGVS c. and p. nomenclature
      • classification, allele frequencies and prediction scores
      • direct links to ClinVar, ClinVitae, Cosmic, ExAc, dbSNP and 1000 Genomes Project
      • newly submitted variants and classifications found by varSEAK users (uploaded in real time)

     

    • Check a variant for effects on splicing:
      • graphical display of the variant and surrounding sequence, including exon/intron structures and splice site features (e.g. branch point)
      • Splice Site Prediction Class and summarized prediction taking into account all surrounding potential splice sites
      • clearly shown scores for relevant potential splice site positions surrounding the variant
      • extended area analysed for 3' variants to cover features such as the branch point or the polypyrimidine tract
      • including the ENT score from MaxEntScan for further comparison

     

  • PRODUCT BROCHURE

    Download our product brochure and
    find out more about our products!

    varSEAK Brochure


  • Search for a gene and find all variants of a gene in one clearly organized table, including:
    • hg19 and hg38 positions
    • HGVS c. and p. nomenclature
    • classification, allele frequencies and prediction scores
    • direct links to ClinVar, ClinVitae, Cosmic, ExAc, dbSNP and 1000 Genomes Project
    • newly submitted variants and classifications found by varSEAK users (uploaded in real time)
  • Check a variant for effects on splicing:
    • graphical display of the variant and surrounding sequence, including exon/intron structures and splice site features (e.g. branch point)
    • Splice Site Prediction Class and summarized prediction taking into account all surrounding potential splice sites
    • clearly shown scores for relevant potential splice site positions surrounding the variant
    • extended area analysed for 3' variants to cover features such as the branch point or the polypyrimidine tract
    • including the ENT score from MaxEntScan for further comparison

Download our product brochure and
find out more about our products!

varSEAK Brochure