Skip Navigation


Nucleic Acids Research Advance Access originally published online on May 25, 2007
Nucleic Acids Research 2007 35(11):3823-3835; doi:10.1093/nar/gkm238
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4686K) Freely available
Right arrow Screen PDF (626K) Freely available
Right arrow Supplementary Material
Right arrowOA All Versions of this Article:
35/11/3823    most recent
gkm238v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (11)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Bromberg, Y.
Right arrow Articles by Rost, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bromberg, Y.
Right arrow Articles by Rost, B.
Related Collections
Right arrow Polymorphism/mutation detection
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2007, Vol. 35, No. 11 3823-3835
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

SNAP: predict effect of non-synonymous polymorphisms on function

Yana Bromberg1,2,4,* and Burkhard Rost1,2,3

1Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th St., 2Columbia University Center for Computational Biology and Bioinformatics (C2B2), 1130 St. Nicholas Ave. Rm. 802, 3NorthEast Structural Genomics Consortium (NESG), 1130 St. Nicholas Ave. Rm. 802 and 4Department of Biomedical Informatics, Columbia University, 630 West 168th St., New York, NY 10032, USA

*To whom correspondence should be addressed. Tel: +1 212 851 4669; Fax: +1 212 305 7932; Email: bromberg{at}rostlab.org, http://www.rostlab.org

Received December 27, 2006. Revised March 28, 2007. Accepted March 30, 2007.

Many genetic variations are single nucleotide polymorphisms (SNPs). Non-synonymous SNPs are ‘neutral’ if the resulting point-mutated protein is not functionally discernible from the wild type and ‘non-neutral’ otherwise. The ability to identify non-neutral substitutions could significantly aid targeting disease causing detrimental mutations, as well as SNPs that increase the fitness of particular phenotypes. Here, we introduced comprehensive data sets to assess the performance of methods that predict SNP effects. Along we introduced SNAP (screening for non-acceptable polymorphisms), a neural network-based method for the prediction of the functional effects of non-synonymous SNPs. SNAP needs only sequence information as input, but benefits from functional and structural annotations, if available. In a cross-validation test on over 80 000 mutants, SNAP identified 80% of the non-neutral substitutions at 77% accuracy and 76% of the neutral substitutions at 80% accuracy. This constituted an important improvement over other methods; the improvement rose to over ten percentage points for mutants for which existing methods disagreed. Possibly even more importantly SNAP introduced a well-calibrated measure for the reliability of each prediction. This measure will allow users to focus on the most accurate predictions and/or the most severe effects. Available at http://www.rostlab.org/services/SNAP


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Hum Mol GenetHome page
M. A. Calton, B. A. Ersoy, S. Zhang, J. P. Kane, M. J. Malloy, C. R. Pullinger, Y. Bromberg, L. A. Pennacchio, R. Dent, R. McPherson, et al.
Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study
Hum. Mol. Genet., March 15, 2009; 18(6): 1140 - 1147.
[Abstract] [Full Text] [PDF]

Home page
 J R Soc InterfaceHome page
G. A Reeves, D. Talavera, and J. M Thornton
Genome and proteome annotation: organization, interpretation and integration
J R Soc Interface, February 6, 2009; 6(31): 129 - 147.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
R. Karchin
Next generation tools for the annotation of human SNPs
Brief Bioinform, January 1, 2009; 10(1): 35 - 52.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Bromberg, G. Yachdav, and B. Rost
SNAP predicts effect of mutations on protein function
Bioinformatics, October 15, 2008; 24(20): 2397 - 2398.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Radivojac, P. H. Baenziger, M. G. Kann, M. E. Mort, M. W. Hahn, and S. D. Mooney
Gain and loss of phosphorylation sites in human cancer
Bioinformatics, August 15, 2008; 24(16): i241 - i247.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Bromberg and B. Rost
Comprehensive in silico mutagenesis highlights functionally important residues in proteins
Bioinformatics, August 15, 2008; 24(16): i207 - i212.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.