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Bioinformatics Advance Access originally published online on June 29, 2006
Bioinformatics 2006 22(17):2183-2185; doi:10.1093/bioinformatics/btl348
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© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs

Joke Reumers , Sebastian Maurer-Stroh , Joost Schymkowitz * and Frederic Rousseau *

Switch Laboratory, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel Pleinlaan 2, Brussels, Belgium

*To whom correspondence should be addressed.

Summary: Single nucleotide polymorphisms (SNPs) constitute the most fundamental type of genetic variation in human populations. About 75 000 of these reported variations cause an amino acid change in the translated protein. An important goal in genomic research is to understand how this variability affects protein function, and whether or not particular SNPs are associated to disease susceptibility. Accordingly, the SNPeffect database uses sequence- and structure-based bioinformatics tools to predict the effect of non-synonymous SNPs on the molecular phenotype of proteins. SNPeffect analyses the effect of SNPs on three categories of functional properties: (1) structural and thermodynamic properties affecting protein dynamics and stability (2) the integrity of functional and binding sites and (3) changes in posttranslational processing and cellular localization of proteins. The search interface of the database can be used to search specifically for polymorphisms that are predicted to cause a change in one of these properties. Now based on the Ensembl human databases, the SNPeffect database has been remodeled to better fit an automatically updatable structure. The current edition holds the molecular phenotype of 74 567 nsSNPs in 23 426 proteins.

Availability: SNPeffect can be accessed through http://snpeffect.vib.be

Supplementary Material: Statistics on the contents of the database, figures on the workflow used to create the database and information on the used sources and tools is available at http://snpeffect.vib.be.

Contact: joost.schymkowitz{at}vub.ac.be or frederic.rousseau{at}vub.ac.be

Received on April 25, 2006; revised on September 9, 2006; accepted on June 22, 2006

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