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Nucleic Acids Research 2006 34(Web Server issue):W651-W655; doi:10.1093/nar/gkl125
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes

Reidar Andreson1,2, Tarmo Puurand1 and Maido Remm1,2,*

1 Department of Bioinformatics, University of Tartu Estonia 2 Estonian Biocentre, Tartu Estonia

*To whom correspondence should be addressed. Tel: +372 7375001; Fax: +372 7420286; Email: maido.remm{at}ut.ee

Received February 14, 2006. Revised February 23, 2006. Accepted March 13, 2006.

SNPmasker is a comprehensive web interface for masking large eukaryotic genomes. The program is designed to mask SNPs from recent dbSNP database and to mask the repeats with two alternative programs. In addition to the SNP masking, we also offer population-specific substitution of SNP alleles in genomic sequence according to SNP frequencies in HapMap Phase II data. The input to SNPmasker can be defined in chromosomal coordinates or inserted as a sequence. The sequences masked by our web server are most useful as a preliminary step for different primer and probe design tasks. The service is available at http://bioinfo.ebc.ee/snpmasker/ and is free for all users.


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