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Briefings in Bioinformatics 2009 10(1):35-52; doi:10.1093/bib/bbn047
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Next generation tools for the annotation of human SNPs

Rachel Karchin

Corresponding author. Rachel Karchin, Biomedical Engineering Department and Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 212218, USA. Tel: +1 410 516 5578; Fax: +1 410 516 5294; E-mail: karchin{at}jhu.edu

Computational biology has the opportunity to play an important role in the identification of functional single nucleotide polymorphisms (SNPs) discovered in large-scale genotyping studies, ultimately yielding new drug targets and biomarkers. The medical genetics and molecular biology communities are increasingly turning to computational biology methods to prioritize interesting SNPs found in linkage and association studies. Many such methods are now available through web interfaces, but the interested user is confronted with an array of predictive results that are often in disagreement with each other. Many tools today produce results that are difficult to understand without bioinformatics expertise, are biased towards non-synonymous SNPs, and do not necessarily reflect up-to-date versions of their source bioinformatics resources, such as public SNP repositories. Here, I assess the utility of the current generation of webservers; and suggest improvements for the next generation of webservers to better deliver value to medical geneticists and molecular biologists.

Keywords: SNP, bioinformatics, prediction methods, webservers, review

Submitted: June 23, 2008. Received (in revised form): August 14, 2008.


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