SNPmasker statistics

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Associated diseases

Associated diseases


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SNPmasker specifications


Unique identifier OMICS_16575
Name SNPmasker
Interface Web user interface
Restrictions to use None
Input data The selected genome and dbSNP version, the genomic sequence, the masking options.
Input format FASTA
Output data The masked sequence, a description of all masked SNPs in given sequence.
Output format FASTA
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes



  • person_outline Reidar Andreson <>

Publication for SNPmasker

SNPmasker in pipelines

PMCID: 4430428
PMID: 25398053
DOI: 10.1038/jid.2014.485

[…] of gja1 mutations and sequencing of parental dna was performed via pcr using kapa 2g fast polymerase (kapa biosystems, woburn, ma) and sanger sequencing. primers were designed with exonprimer and snpmasker to specifically amplify gja1 and not its pseudogene., a gja1 cdna clone was obtained (hscd00332741, harvard plasmid, brookline, ma) and subcloned into pcdna3.1(-) zeo (invitrogen, carlsbad, […]

PMCID: 3709244
PMID: 22515571
DOI: 10.1111/j.1525-1470.2012.01757.x

[…] boundaries, were generated with primer3 ( using the hg18 version of the genome masked to exclude dna sequence repeats (genomemasker: as the template. we also generated primers for the five most common filaggrin mutations in european populations (r501x, 2282del4, 3702delg, r2447x, and s3247x) () and for the previously […]

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SNPmasker in publications

PMCID: 3411792
PMID: 22879986
DOI: 10.1371/journal.pone.0042439

[…] sequences between fcgrs, the specificity sequences were checked with the sequence databases using blast ( these sequences were also verified by snpmasker1.1 ( to make sure that the different bases were caused by snp . and each primer pair was tested for potential primer-dimer and hairpin structures using […]

PMCID: 3334619
PMID: 22185227
DOI: 10.1186/gb-2011-12-12-r124

[…] significant somatic mutations for functional consequences, we used annovar [] on hg19., for each snp a region ± 300 bp surrounding the site was downloaded from the ucsc genome browser (hg19). snpmasker 1.0 [] (hg19 and dbsnp build 132) was used to mask variant alleles in each sequence to avoid introducing allele bias in the pcr primers. pcr primers (table s10 in additional file ) […]

PMCID: 2741440
PMID: 19715565
DOI: 10.1186/1472-6750-9-75

[…] due to snps present in primer binding sites., the best approach to developing pcr assays that are insensitive to snps is to avoid them during oligonucleotide design by using software, such as snpmasker [], designed for this purpose. currently, there are over 50 million snp submissions to consider for the human genome in build 129 of dbsnp . twenty-seven percent of those have been added […]

PMCID: 2684120
PMID: 19379518
DOI: 10.1186/1755-8794-2-17

[…] that had an association with at least one disease in two separate preferably caucasian populations was then allowed to progress to the next step., finally each polymorphism was masked using snpmasker and evaluated for ease of adaptation to the sequenom platform. the remaining polymorphisms were used in the sequenom assay design 3.1 [] program to develop a large multiplex assay. several […]

PMCID: 2475630
PMID: 18539607
DOI: 10.1093/nar/gkn357

[…] genometester 1.3 (), which predicted generation of a single product (up to 1000 bp) per primer pair based on the human genome. primer sequences were further assessed for the presence of snps using snpmasker software (). apex-2 primers were generated upon addition of a universal sequence (5′-gatcaggcgtctgtcgtgctc-3′) to the 5′ end of each snp-specific primer. apex-2 primers were then amino […]

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SNPmasker institution(s)
Department of Bioinformatics, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia
SNPmasker funding source(s)
This work was supported by the Estonian Ministry of Education and Research grant 0182649s04, grant 6041 from Estonian Science Foundation and grant EU19730 from Enterprise Estonia.

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