PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

doi:10.1093/bioinformatics/btv195

. 2015 Aug 15;31(16):2745-7.

doi: 10.1093/bioinformatics/btv195. Epub 2015 Apr 6.

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

Yongwook Choi¹, Agnes P Chan¹

Affiliations

PMID: 25851949
PMCID: PMC4528627
DOI: 10.1093/bioinformatics/btv195

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

Yongwook Choi et al. Bioinformatics. 2015.

. 2015 Aug 15;31(16):2745-7.

doi: 10.1093/bioinformatics/btv195. Epub 2015 Apr 6.

Authors

Yongwook Choi¹, Agnes P Chan¹

Affiliation

¹ The J. Craig Venter Institute, Rockville, MD 20850, USA.

PMID: 25851949
PMCID: PMC4528627
DOI: 10.1093/bioinformatics/btv195

Abstract

We present a web server to predict the functional effect of single or multiple amino acid substitutions, insertions and deletions using the prediction tool PROVEAN. The server provides rapid analysis of protein variants from any organisms, and also supports high-throughput analysis for human and mouse variants at both the genomic and protein levels.

Availability and implementation: The web server is freely available and open to all users with no login requirements at http://provean.jcvi.org.

Contact: achan@jcvi.org

Supplementary information: Supplementary data are available at Bioinformatics online.

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References

1. Adzhubei I.A., et al. . (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248–249. - PMC - PubMed
1. Choi Y. (2012) A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine ACM, Orlando, Florida, pp. 414–417.
1. Choi Y., et al. . (2012) Predicting the functional effect of amino acid substitutions and indels. PloS one, 7, e46688. - PMC - PubMed
1. Cooper G.M., Shendure J. (2011) Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet., 12, 628–640. - PubMed
1. Kumar P., et al. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073–1081. - PubMed

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[1] Adzhubei I.A., et al. . (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248–249. - PMC - PubMed

[2] Adzhubei I.A., et al. . (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248–249. - PMC - PubMed

[3] Choi Y. (2012) A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine ACM, Orlando, Florida, pp. 414–417.

[4] Choi Y. (2012) A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine ACM, Orlando, Florida, pp. 414–417.

[5] Choi Y., et al. . (2012) Predicting the functional effect of amino acid substitutions and indels. PloS one, 7, e46688. - PMC - PubMed

[6] Choi Y., et al. . (2012) Predicting the functional effect of amino acid substitutions and indels. PloS one, 7, e46688. - PMC - PubMed

[7] Cooper G.M., Shendure J. (2011) Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet., 12, 628–640. - PubMed

[8] Cooper G.M., Shendure J. (2011) Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet., 12, 628–640. - PubMed

[9] Kumar P., et al. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073–1081. - PubMed

[10] Kumar P., et al. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073–1081. - PubMed

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PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

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PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

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