Analyze Cancer-Associated Variants

Enter Your Mutations:

Input Format:

Our software and server accepts one of the following formats (see here for annotating VCF files):

  • <protein> <substitution>
  • dbSNP rs identifiers

Where <protein> is the protein identifier and <substitution> is the amino acid substitution in the conventional one letter format. Multiple substitutions can be entered on a single line and should be separated by a comma. Our server accepts SwissProt/TrEMBL, RefSeq and Ensembl protein identifiers, e.g.:

P43026 L441P
ENSP00000325527 N548I,E1073K,C2307S 

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Prediction Threshold:

As described in our paper, our server uses a default prediction threshold of -0.75. Here, predictions with scores less than this indicate that the mutation is potentially associated with cancer; however, our prediction threshold this can be adjusted and tuned to cater for your individual needs. For example, if you are interested in minimising the number of false positives in your analysis, then you should opt for a more conservative threshold, e.g. -3.0; however, if you are interested in capturing a large proportion of cancer-associated mutations (regardless of the number of false positives), then a less stringent threshold should be selected, e.g. 0.0 or higher. To inform you of this choice, the specificity and sensitivity of our software at various prediction thresholds can be seen using the below interactive graph:

Prediction Threshold

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