BatchPrimer3: a high throughput web application for PCR and sequencing primer design.
BatchPrimer3: a high throughput web application for PCR and sequencing primer design.
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DOI：
10.1186/1471-2105-9-253
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发表时间：
2008-05-29
影响因子：
3
通讯作者：
Anderson OD
中科院分区：
文献类型：
--
作者：
You FM;Huo N;Gu YQ;Luo MC;Ma Y;Hane D;Lazo GR;Dvorak J;Anderson OD
微卫星（SSR）标记和单核苷酸多态性（SNP）标记是两种重要的遗传标记，可用于遗传作图和基因分型。通常，大规模基因组研究项目需要高通量计算机辅助引物设计。许多这样的基于网络或标准单独的程序为PCR引物设计是可用的，但在质量和功能各不相同。特别是，大多数程序缺乏批量引物设计能力。越来越需要这样一种高通量的软件工具来设计SSR侧翼引物和SNP基因分型引物。基于Primer3开发了一个新的网页引语设计程序BatchPrimer3。BatchPrimer3采用Primer3核心程序作为主要引物设计引擎，选择最佳引物对。在BatchPrimer3中加入了一个新的基于分数的引物选择模块，用于选择位置受限的引物。BatchPrimer3 v1.0实现了几种类型的引物设计，包括通用引物、SSR引物以及SSR检测、SNP基因分型引物（包括单碱基延伸引物、等位基因特异性引物和用于四引物ARMS PCR的四引物）以及DNA测序引物。FASTA格式的DNA序列可以批量读取到程序中。通过序列的预分析，可以获得输入序列的基本信息，作为引物设计参数设置的参考。输入序列可以预处理和屏蔽，以排除和/或包括特定区域，或为不同的引物设计目的设置目标，如Primer3Web和primer3Plus。制表符分隔或excel格式的引物输出也极大地方便了后续的引物排序过程。利用该程序设计了数千条引物，包括小麦保守内含子侧翼引物、小麦基因组特异性SNP基因分型引物和短柄草SSR侧翼引物，并在多个实验室进行了验证。BatchPrimer3是一个综合性的网页引物设计程序，以高通量的方式开发不同类型的引物。引物设计的其他方法可以很容易地集成到BatchPrimer3的未来版本。该程序的源代码和数以千计的PCR和测序引物为小麦和短柄草设计。
Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at .
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影响因子：
2.9
作者：
Huo, Naxin;Lazo, Gerard R.;Gu, Yong Q.
通讯作者：
Gu, Yong Q.
影响因子：
3.3
作者：
Qi, LL;Echalier, B;Gill, BS
通讯作者：
Gill, BS
影响因子：
3.3
作者：
Ruiz-Sanz, Jose Ignacio;Aurrekoetxea, Igor;Ruiz-Larrea, Maria Begona
通讯作者：
Ruiz-Larrea, Maria Begona
影响因子：
2.4
作者：
Leyva-Baca, I.;Schenkel, F.;Karrow, N. A.
通讯作者：
Karrow, N. A.
影响因子：
5.8
作者：
Koressaar, Triinu;Remm, Maido
通讯作者：
Remm, Maido