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 http://elixir.ut.ee/Main/Services.
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]
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