SNPmasker

SNPmasker masks single nucleotide polymorphisms (SNPs) and low-complexity or repetitive regions in large eukaryotic genomes to prepare sequences for downstream analyses such as primer and probe design and population-specific studies.

Key Features:

• SNP Masking: Masks SNPs using entries from the dbSNP database.
• Repeat Masking: Employs two alternative programs to mask repetitive elements and low-complexity regions.
• Population-Specific Substitution: Performs allele substitution based on population frequencies from HapMap Phase II.
• Flexible Input Options: Accepts input as chromosomal coordinates or as direct sequence data.
• Primer and Probe Design Support: Produces masked sequences intended for use in primer and probe design workflows.

Scientific Applications:

• Genomic Research: Prepares large eukaryotic genome sequences free of SNPs and repeats for downstream analyses.
• Population Genetics: Enables population-specific sequence analyses through HapMap Phase II–based allele substitution.
• Molecular Biology: Provides masked sequences for designing primers and probes for PCR, qPCR, and related assays.

Methodology:

Masks SNPs using dbSNP entries; masks repetitive and low-complexity regions via two alternative masking programs; performs population-specific allele substitution using HapMap Phase II frequencies; accepts chromosomal coordinates or direct sequence input.