Format

Send to

Choose Destination
Methods Mol Biol. 2015;1275:1-16. doi: 10.1007/978-1-4939-2365-6_1.

Fast masking of repeated primer binding sites in eukaryotic genomes.

Author information

1
Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010, Estonia.

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/.

PMID:
25697648
DOI:
10.1007/978-1-4939-2365-6_1
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Springer
Loading ...
Support Center