真核生物基因组中重复引物结合位点的快速屏蔽

Fast masking of repeated primer binding sites in eukaryotic genomes.

作者信息

Andreson Reidar, Kaplinski Lauris, Remm Maido

机构信息

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

出版信息

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

DOI:10.1007/978-1-4939-2365-6_1

PMID:25697648

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/.

摘要

在本文中，我们描述了GenomeMasker的工作原理及一系列实际应用。GenomeMasker是一个能在全测序基因组中查找并屏蔽所有重复DNA基序的程序。它会详尽地在研究的基因组中查找并屏蔽所有重复DNA基序。该软件针对PCR引物设计进行了优化。其算法专为高通量工作而设计，能够屏蔽大片段DNA区域，甚至是整个真核生物基因组。此外，该软件还能为数千个候选PCR引物对预测研究基因组中的所有替代性PCR产物。文中展示了GenomeMasker命令行版本的实际应用，该版本可从http://bioinfo.ut.ee/download/下载。在http://bioinfo.ut.ee/genometester/和http://bioinfo.ut.ee/snpmasker/上可获取选项有限的图形化网络界面。