GSP：一个基于网络的平台，用于在多倍体中设计基因组特异性引物。
GSP: a web-based platform for designing genome-specific primers in polyploids.
机构信息
USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
出版信息
Bioinformatics. 2016 Aug 1;32(15):2382-3. doi: 10.1093/bioinformatics/btw134. Epub 2016 Mar 9.
MOTIVATION
The sequences among subgenomes in a polyploid species have high similarity, making it difficult to design genome-specific primers for sequence analysis.
RESULTS
We present GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in existing databases, performs a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primers diagram, a sequence alignment viewer and a virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users.
AVAILABILITY AND IMPLEMENTATION
GSP is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/GSP Source code and command-line application are available at https://github.com/bioinfogenome/GSP CONTACTS: yong.gu@ars.usda.gov or devin.coleman-derr@ars.usda.gov
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
多倍体物种中亚基因组之间的序列具有高度相似性，因此难以设计用于序列分析的基因组特异性引物。
结果
我们提出了 GSP，这是一个基于网络的平台，用于设计基因组特异性引物，以区分多倍体基因组中的亚基因组序列。GSP 使用 BLAST 从现有数据库中提取亚基因组的同源序列，进行多序列比对，并根据比对中的序列变异设计引物。交互式引物图、序列比对查看器和虚拟电泳作为引物设计结果的一部分显示。GSP 还可以根据用户上传的多个序列设计特定的引物。
可用性和实现
GSP 是一个用户友好且高效的网络平台，可免费在 http://probes.pw.usda.gov/GSP 上访问。源代码和命令行应用程序可在 https://github.com/bioinfogenome/GSP 上获得。
联系人
yong.gu@ars.usda.gov 或 devin.coleman-derr@ars.usda.gov
补充信息
补充数据可在 Bioinformatics 在线获得。
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