PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important.

The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2 [1]. Read more.

A fast computation approach to obtain pairwise sequence alignment scores enabled the generation of precomputed PROVEAN predictions for 50 possible variations (20 single AA substitutions, 20 single AA insertions, and 1-10 AA deletions) at every amino acid position of all human protein sequences [2].

This work is funded by the National Institutes of Health [grant number 5R01HG004701-04].

  1. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the Functional Effect of Amino Acid Substitutions and Indels. PLoS ONE 7(10): e46688.
  2. Choi Y (2012) A Fast Computation of Pairwise Sequence Alignment Scores Between a Protein and a Set of Single-Locus Variants of Another Protein. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB '12). ACM, New York, NY, USA, 414-417.
    (* This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in ACM BCB '12.

PROVEAN web server functions are currently using PROVEAN v1.1.3.




This tool provides PROVEAN prediction for a protein sequence from any organisms.

  • Input: A protein sequence from any organism and amino acid variants of interest. See example.
  • Output: PROVEAN scores and predictions. See example.

PROVEAN Human Protein Batch

This tool provides PROVEAN and SIFT predictions for a list of human protein variants.

  • Input: A list of human protein variants. See example.
  • Output: Scores and predictions from PROVEAN and SIFT. See example.

PROVEAN Human Genome Variants

This tool provides PROVEAN and SIFT predictions for a list of human genome variants. It is based on the human assembly GRCh37 and genome annotation Ensembl 66.

  • Input: A list of human genomic coordinates and sequence variants of interests. See example.
  • Output: Changes at protein level, their scores and predictions from PROVEAN and SIFT. See example.