BatchPrimer3: A high throughput web application for PCR and sequencing primer design
By F. You, N. Huo, Yong Qiang Gu, Ming-Cheng Luo, Yaqin Ma, D. Hane, G. Lazo, J. Dvorak, O. Anderson. BMC Bioinformatics, 2008
813 citations recorded by the source corpus.
BackgroundMicrosatellite (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.ResultsA 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.ConclusionBatchPrimer3 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 http://wheat.pw.usda.gov/demos/BatchPrimer3/.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/70a1b22cdc269286a9f928b4f3f0fdf96c00d3d5
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In Genetics
In Molecular Biology
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Citations in the corpus
- QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR (2008, neutral): “There are surprisingly few free software packages available to the academic research community suitable for the design of primer pairs for such high-throughput projects, for online use or download, including Osprey [5], Primique [6] and a few interfaces to Primer3 [7] such as Primer3Plus [8], AutoPr”
- PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update (2011, background): “Multiple design algorithms have been proposed (7–10), but few of them have been validated experimentally.”
- PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification (2009, background): “A large number of tools and resources are available that can be used for designing PCR primers for various applications (56–67).”
- Primer3—new capabilities and interfaces (2012, background): “The BatchPrimer3 web service (12) allows high-throughput primer design from a list of target sequences and also extends Primer3’s selection methods with a focus on SNP typing.”
- Mapping QTL for heat tolerance at flowering stage in rice using SNP markers (2012, methodology): “1 were designed using BatchPrimer3 (You et al. 2008) for screening the BC2F2 population.”