Nucleic Acids Research, 2006, Vol. 34, Web Server issue W653 Figure 1. Web interface for SNPmasker input. ability to reject the primer candidates ending with a lower-case letter. EXAMPLES SNPmasker is primarily designed for masking the sequences before primer and probe design. The exact masking style may vary depending on the purpose and on the technology requirements. Here are some examples of using SNPmasker for different purposes. For illustration we have used a region from human the chromosome 2, nucleotides 19 341 544–519 342 344. This region contains several SNPs and repeated regions. If one is interested in the PCR primer design for a genomic PCR, then the best masking style is ‘N’ masking for SNPs and strand-speciﬁc lower-case masking for the repeats. When used together with GM_Primer3 program, this masking style