title: Fast masking of repeated primer binding sites in eukaryotic genomes.
abstract: 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 http://bioinfo.ut.ee/download/. Graphical Web interfaces with limited options are available at http://bioinfo.ut.ee/genometester/ and http://bioinfo.ut.ee/snpmasker/.
authors.affiliation: Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010, Estonia.
authors.forename: Reidar
authors.initials: R
authors.lastname: Andreson
authors.forename: Lauris
authors.initials: L
authors.lastname: Kaplinski
authors.forename: Maido
authors.initials: M
authors.lastname: Remm
mesh_terms: D000465:Algorithms; D001665:Binding Sites / Q000235:genetics; D017931:DNA Primers / Q000378:metabolism*; D005057:Eukaryotic Cells / Q000378:metabolism*; D016678:Genome / Q000235:genetics*; D012984:Software
chemical_list: D017931:DNA Primers