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Overview | |
Primer Design Server 1 (Albany) | |
Primer Resources | |
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Last modified on Dr. Frank M. You frank.you@canada.ca |
Genomics & Gene Discovery |
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BatchPrimer3 is a comprehensive web primer design program using Primer3 core program as a major primer design engine to design different types of PCR primers and sequencing primers in a high-through manner. BatchPrimer3 allows users to design several types of primers including generic primers, hybridization oligos, 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. A batch input of large number of sequences and a tab-delimited result output greatly facilitates rapid primer design and ordering process. The BatchPrimer3 paper is available in BMC Bioinformatics. The citation is: Frank M You, Naxin Huo, Yong Qiang Gu, Ming-cheng Luo, Yaqin Ma, Dave Hane, Gerard R Lazo, Jan Dvorak and Olin D Anderson. BatchPrimer3: a high throughput web application for PCR and sequencing primer designi. BMC Bioinformatics 2008, 9:253, doi:10.1186/1471-2105-9-253 [PubMed] [BMC Bioinformatics] Primer design serversPrimer design methodsIn BatchPrimer3 1.0, several types of primer design are implemented:
Sequence InputTwo ways are available to input sequences:
Sequence pre-analysisA utility tool for pre-analysis of input sequences is provided in BatchPrimer3 to help users to understand the basic statistics of input sequences, such as sequence length, GC content and their distributions in a whole set of input sequences. The information provides hints to adjust the parameter ranges of product size and GC content. See example.Result outputThe BatchPrimer3 program produces four parts of outputs:
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