PolyMarker: A fast polyploid primer design pipeline.
PolyMarker: A fast polyploid primer design pipeline.
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DOI：
10.1093/bioinformatics/btv069
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发表时间：
2015-06-15
期刊：
影响因子：
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通讯作者：
Caccamo M
中科院分区：
文献类型：
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作者：
Ramirez-Gonzalez RH;Uauy C;Caccamo M
概述：遗传标记的设计在作物育种计划中特别相关。尽管许多经济上重要的作物是多倍体生物，但目前的引物设计工具是针对二倍体物种定制的。例如，面包小麦是由三个相关基因组组成的六倍体，如果引物不是基因组特异性的，遗传标记的性能就会降低。PolyMarker是一种通过使用局部比对和标准引物设计工具为指定基因组选择候选引物来生成SNP标记的管道，以测试引物的可行性。社区可以使用命令行工具和Web界面。可用性和实施：PolyMarker作为红宝石BioGem：bio-polyploid-tools提供。网页界面：http://polymarker.tgac.ac.uk。联系人：Ricardo. tgac.ac.uk补充信息：补充数据可在生物信息学在线获得。
Summary: The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished if the primers are not genome specific. PolyMarker is a pipeline that generates SNP markers by selecting candidate primers for a specified genome using local alignments and standard primer design tools to test the viability of the primers. A command line tool and a web interface are available to the community. Availability and implementation: PolyMarker is available as a ruby BioGem: bio-polyploid-tools. Web interface: http://polymarker.tgac.ac.uk. Contact: Ricardo.Ramirez-Gonzalez@tgac.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.