引物设计-M：一种基于多序列比对的多引物设计工具，用于跨越可变基因组。
PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.
作者信息
Yoon Hyejin, Leitner Thomas
机构信息
Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
出版信息
Bioinformatics. 2015 May 1;31(9):1472-4. doi: 10.1093/bioinformatics/btu832. Epub 2014 Dec 17.
SUMMARY
Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions.
AVAILABILITY AND IMPLEMENTATION
PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html
CONTACT
摘要
对整个病毒基因组或线粒体DNA（mtDNA）进行分析需要针对其基因组全面设计许多引物。此外，同时优化多个DNA引物设计标准可能会提高整体实验效率和下游生物信息学处理能力。为实现这些目标，我们开发了PrimerDesign-M。它包括多种用于多引物设计的选项，使研究人员能够高效设计覆盖长DNA靶标的步移引物，如完整的HIV-1基因组，并能根据多序列比对中的遗传多样性和用户给出的实验设计限制同时优化引物。PrimerDesign-M还可以设计包含DNA条形码并尽量减少引物二聚化的引物。PrimerDesign-M能为高度可变的DNA靶标找到最佳引物，并通过提供替代设计以适应实验条件来促进设计灵活性。
可用性与实现方式
PrimerDesign-M可作为网络工具在http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html获取。
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