Our software and server accepts one of the following formats (see here for annotating VCF files):
<protein> <substitution>
dbSNP rs identifiers
<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
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: