SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.
SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.
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SOP3v2：基于网络的寡核苷酸引物三组选择，用于人类和小鼠多态性的基因分型。
DOI：
10.1093/nar/gki483
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发表时间：
2005
期刊：
影响因子：
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通讯作者：
Trucco,Massimo
中科院分区：
文献类型：
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作者：
Ringquist,Steven;Pecoraro,Christopher;Gilchrist,CrystalMS;Styche,Alexis;Rudert,WilliamA;Benos,PanagiotisV;Trucco,Massimo
SOP 3v 2是一种数据库驱动的图形化基于Web的应用程序，用于促进基因分型检测试剂盒设计。SOP 3v 2接受多种形式的数据输入，包括基因名称、参考序列号和物理位置。对于每个条目，应用程序提供了一组推荐的正向和反向PCR引物，沿着测序引物，该引物针对基于序列的基因分型测定进行了优化。SOP 3v 2生成的寡核苷酸引物三联体能够分析基因组DNA中发现的单核苷酸多态性（SNP）以及插入/缺失多态性。该应用程序的数据库由来自国家生物技术信息中心（NCBI）dbSNP数据库的仓储信息、来自人类和小鼠的基因组DNA序列以及LocusLink基因属性信息生成。查询结果可以根据其生物相关性进行排序，例如非同义编码变化或物理位置。人类多态性查询可以指定种族、单体型和验证状态。使用SOP 3v 2的核心算法开发引物，用于通过稳定性试验评价候选引物，适用于需要基因座特异性扩增的基于序列的基因分型方法。该方法已经过实验室验证。在测试的SOP 3v 2设计的引物三组中，大多数（>80%）已成功产生基因分型数据。该应用程序可以通过网站http://imgen.ccbb.pitt.edu/sop3v2访问。
SOP3v2 is a database-driven graphical web-based application for facilitating genotyping assay design. SOP3v2 accepts data input in numerous forms, including gene names, reference sequence numbers and physical location. For each entry, the application presents a set of recommended forward and reverse PCR primers, along with a sequencing primer, which is optimized for sequence-based genotyping assays. SOP3v2-generated oligonucleotide primer trios enable analysis of single nucleotide polymorphisms (SNPs) as well as insertion/deletion polymorphisms found in genomic DNA. The application's database was generated by warehousing information from the National Center for Biotechnology Information (NCBI) dbSNP database, genomic DNA sequences from human and mouse, and LocusLink gene attribute information. Query results can be sorted by their biological relevance, such as nonsynonymous coding changes or physical location. Human polymorphism queries may specify ethnicity, haplotype and validation status. Primers are developed using SOP3v2's core algorithm for evaluating primer candidates through stability tests and are suitable for use with sequence-based genotyping methods requiring locus-specific amplification. The method has undergone laboratory validation. Of the SOP3v2-designed primer trios that were tested, a majority (>80%) have successfully produced genotyping data. The application may be accessed via the web at http://imgen.ccbb.pitt.edu/sop3v2 .