Functionality of curated missense mutations in tumor suppressor genes dependent upon user knowledge and process when using existing algorithms SIFT, Align-GVGD, PolyPhen-2 and Xvar.
"Accurately predicting the impact of missense mutations on protein function depends on the algorithm used, the type of sequence alignment provided, and on the number of sequences in the alignment. In addition to problems of interpretation there are technical difficulties as well. In our experience, when simply submitting a list of missense mutations to an algorithm the user must be able to: (1) manipulate the input format specified by each algorithm, (2) build an optimal protein sequence alignment, if required, (3) be knowledgeable of Unix system commands, (4) interpret server error messages, and (5) transform the output to a working format for further studies."
Hicks S, et al. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Human Mutation 2011, 32(6): 661–8.
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