Skip Navigation


Nucleic Acids Research Advance Access originally published online on December 17, 2007
Nucleic Acids Research 2008 36(Database issue):D825-D829; doi:10.1093/nar/gkm979
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1560K) Freely available
Right arrow Screen PDF (267K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
36/suppl_1/D825    most recent
gkm979v1
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 PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Citing Articles
Right arrowScopus Links
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Reumers, J.
Right arrow Articles by Schymkowitz, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Reumers, J.
Right arrow Articles by Schymkowitz, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2008, Vol. 36, Database issue D825-D829
© 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.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases

Joke Reumers1,2, Lucia Conde3, Ignacio Medina3, Sebastian Maurer-Stroh1,2, Joost Van Durme1,2, Joaquin Dopazo3,4, Frederic Rousseau1,2 and Joost Schymkowitz1,2,*

1Switch Laboratory, Department of Applied Biological Sciences, Vrije Universiteit Brussel, 2Switch Laboratory, VIB, Pleinlaan 2, 1050 Brussel, Belgium, 3Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF) and 4Functional Genomics Node, INB, CIPF, Valencia 46013, Spain

*To whom correspondence should be addressed. Tel: +32 2 629 14 25; Fax: +32 2 629 19 63; E-mail: joost.schymkowitz{at}vub.ac.be

Correspondence may also be addressed to Frederic Rousseau. Tel: +32 2 629 14 25; Fax: +32 2 629 19 63; E-mail: frederic.rousseau{at}vub.ac.be

Received September 15, 2007. Revised October 17, 2007. Accepted October 18, 2007.

Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutations in groups of patients and control individuals, the distinction between disease causing mutation and polymorphism is often unclear. Annotation of the functional and structural implications of single nucleotide changes thus provides valuable information to interpret and guide experiments. The SNPeffect and PupaSuite databases are now synchronized to deliver annotations for both non-coding and coding SNP, as well as annotations for the SwissProt set of human disease mutations. In addition, SNPeffect now contains predictions of Tango2: an improved aggregation detector, and Waltz: a novel predictor of amyloid-forming sequences, as well as improved predictors for regions that are recognized by the Hsp70 family of chaperones. The new PupaSuite version incorporates predictions for SNPs in silencers and miRNAs including their targets, as well as additional methods for predicting SNPs in TFBSs and splice sites. Also predictions for mouse and rat genomes have been added. In addition, a PupaSuite web service has been developed to enable data access, programmatically. The combined database holds annotations for 4 965 073 regulatory as well as 133 505 coding human SNPs and 14 935 disease mutations, and phenotypic descriptions of 43 797 human proteins and is accessible via http://snpeffect.vib.be and http://pupasuite.bioinfo.cipf.es/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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
 Circ Cardiovasc GenetHome page
A. P. Reiner, M. D. Gross, C. S. Carlson, S. J. Bielinski, L. A. Lange, M. Fornage, N. S. Jenny, J. Walston, R. P. Tracy, O. D. Williams, et al.
Common Coding Variants of the HNF1A Gene Are Associated With Multiple Cardiovascular Risk Phenotypes in Community-Based Samples of Younger and Older European-American Adults: The Coronary Artery Risk Development in Young Adults Study and The Cardiovascular Health Study
Circ Cardiovasc Genet, June 1, 2009; 2(3): 244 - 254.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
L. Quaye, D. Dafou, S. J. Ramus, H. Song, A. G. Maharaj, M. Notaridou, E. Hogdall, S. K. Kjaer, L. Christensen, C. Hogdall, et al.
Functional complementation studies identify candidate genes and common genetic variants associated with ovarian cancer survival
Hum. Mol. Genet., May 15, 2009; 18(10): 1869 - 1878.
[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.