Bioinformatics Advance Access published online on June 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl348
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1 Switch Laboratory, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
* To whom correspondence should be addressed.
Summary: Single nucleotide polymorphisms constitute the most fundamental type of genetic variation in human populations. About 75000 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 74567 nsSNPs in 23426 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.
Received April 25, 2006
Revised June 14, 2006
Accepted June 22, 2006
Applications note
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non synonymous SNPs
Joke Reumers 1,
Sebastian Maurer-Stroh 1,
Joost Schymkowitz 1,
and
Frederic Rousseau 1 *
Frederic Rousseau, E-mail: frederic.rousseau{at}vub.ac.be
Abstract
Associate Editor: Jonathan Wren
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