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Bioinformatics Advance Access originally published online on December 19, 2008
Bioinformatics 2009 25(5):655-661; doi:10.1093/bioinformatics/btn653
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© 2008 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.

SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms

Claude Chelala *, Arshad Khan and Nicholas R Lemoine

Centre for Molecular Oncology and Imaging, Institute of Cancer & CR-UK Clinical Centre, Barts & The London School of Medicine (QMUL), Charterhouse Square, London EC1M 6BQ, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: Design a new computational tool allowing scientists to functionally annotate newly discovered and public domain single nucleotide polymorphisms in order to help in prioritizing targets in further disease studies and large-scale genotyping projects.

Summary: SNPnexus database provides functional annotation for both novel and public SNPs. Possible effects on the transcriptome and proteome levels are characterized and reported from five major annotation systems providing the most extensive information on alternative splicing. Additional information on HapMap genotype and allele frequency, overlaps with potential regulatory elements or structural variations as well as related genetic diseases can be also retrieved. The SNPnexus database has a user-friendly web interface, providing single or batch query options using SNP identifiers from dbSNP as well as genomic location on clones, contigs or chromosomes. Therefore, SNPnexus is the only database currently providing a complete set of functional annotations of SNPs in public databases and newly detected from sequencing projects. Hence, we describe SNPnexus, provide details of the query options, the annotation categories as well as biological examples of use.

Availability: The SNPnexus database is freely available at http://www.snp-nexus.org.

Contact: claude.chelala{at}cancer.org.uk

Associate Editor: Alex Bateman

Received on September 29, 2008; revised on November 25, 2008; accepted on December 17, 2008

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