SNPmasker 1.1

About the program:

SNPmasker 1.1 is a program to mask all SNPs in given sequence using information of dbSNP. Additionally it is possible to mask all non-unique words using GenomeMasker module. It allows masking of the entire template DNA before primer design to avoid consideration of poor primer candidates. GenomeMasker is able to identify and mask repeating words that have not included in current repeat libraries. This, combined with a specific 3'-end masking technique, allowed us to achieve more sensitive masking than existing approaches. Index file for masking repeats is created with word length 16 and binding cutoff 10 (all 16 bp words appearing more than 10 times in genome will be masked by GenomeMasker). Stand-alone GenomeMasker binaries, example files and README are available here.

SNPmasker may take some time to work, so You may want to bookmark the results page or write down the results ID and come back later. If You enter Your email address, results ID will be sent to You when ready.

Here is a correct input file.

For further information please contact: and please check the HELP page too.

SNPmasker is a part of services provided by ELIXIR - European research infrastructure for biological information. For other services provided by ELIXIR's Estonian Node visit

How to cite SNPmasker: Andreson R, Puurand T, Remm M. SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. Nucleic Acids Res. 2006 Jul 1;34: W651-5. [PubMed] [Full Text]

There have been 156177 submissions to this web site since November 2005.

Please select genome and dbSNP version:
Please insert a region coordinates, paste sequence or select input file:
Chromosome: Start position: End position:

or paste sequence below:

Allowed characters in sequence: A,C,G,T,N,a,c,g,t,n. Other characters are converted to N. Numbers and blanks are ignored. FastA format is allowed.

or select Your input file in FastA format (plain .txt file only!):
Mask SNPs with symbol:
With 'N' symbol (default)
With lower-case letter
With IUPAC symbol
With custom symbol ->
Mask SNPs based on major/minor allele frequency (HUMAN ONLY!):
Replace with upper-case letter using HapMap3 major allele frequency
Replace with lower-case letter using HapMap3 major allele frequency


HapMap3 major allele frequency cutoff: %

HapMap3 major allele callrate cutoff: %
Mask SNPs based on heterozygosity or validation:
Global minor allele frequency (MAF): (0-0.5 eg. 0.497)

Heterozygosity of a SNP: (0-0.75 eg. 0.1)

SNP validation info:
Repeat-masking options: GenomeMasker options:
GenomeMasker with lower-case letters (default)
GenomeMasker with custom letter ->
RepeatMasker with lower-case letters
NO repeat-masking
BOTH strands (default)
FORWARD strand only
REVERSE strand only
Outside TARGET region
This type masks upper strand in front of target region and lower strand behind the target region. FROM and TO define start and end nucleotides of the target region (NOT an absolute positions in chromosome!).

From: to:

Number of bp to mask:
(from 3' end of repeats)
If you enter Your email address, You will get an email when SNPmasker job is finished (optional):