Fast Masking of Repeated Primer Binding Sites in Eukaryotic Genomes

  • Reidar Andreson
  • Lauris Kaplinski
  • Maido RemmEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1275)


In this article we describe the working principle and a list of practical applications for GenomeMasker—a program that finds and masks all repeated DNA motifs in fully sequenced genomes. The GenomeMasker exhaustively finds and masks all repeated DNA motifs in studied genomes. The software is optimized for PCR primer design. The algorithm is designed for high-throughput work, allowing masking of large DNA regions, even entire eukaryotic genomes. Additionally, the software is able to predict all alternative PCR products from studied genomes for thousands of candidate PCR primer pairs.

Practical applications of the GenomeMasker are shown for command-line version of the GenomeMasker, which can be downloaded from Graphical Web interfaces with limited options are available at and

Key words

PCR DNA repeats Primer design Microarrays DNA masking 



The development of GenomeMasker package was supported by the Estonian Ministry of Education and Research grant 0182649s04 and grant EU19730 from Enterprise Estonia. Development of primer design software in our group has been funded by Centre of Excellence in Genomics at Estonian Biocentre (EU European Regional Development Fund). The authors thank Katre Palm for a valuable help with English grammar.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Reidar Andreson
    • 1
    • 2
  • Lauris Kaplinski
    • 1
    • 2
  • Maido Remm
    • 1
    • 2
    Email author
  1. 1.Department of BioinformaticsUniversity of TartuTartuEstonia
  2. 2.Estonian BiocentreTartuEstonia

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