ArticleBMC genomics2009
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Identification of Reference Genes for RT-qPCR Assays inCurrent issues in molecular biology · 2026Article
- Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era.Methods in molecular biology (Clifton, N.J.) · 2021Review
- PrimedRPA: primer design for recombinase polymerase amplification assays.Bioinformatics (Oxford, England) · 2019Article
- PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization.BMC bioinformatics · 2018Article
- PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.Nucleic acids research · 2014Article
- PD5: a general purpose library for primer design software.PloS one · 2013Article
- Primer3--new capabilities and interfaces.Nucleic acids research · 2012Article
- microPIR: an integrated database of microRNA target sites within human promoter sequences.PloS one · 2012Article
- Extending Asia Pacific bioinformatics into new realms in the "-omics" era.BMC genomics · 2009Article
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundPolymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools for primer design do not adequately address the problem of PCR failure due to mis-priming on target-related sequences and structural variations in the genome.
methodsWe have developed an integrated graphical web-based application for primer design, called RExPrimer, which was written in Python language. The software uses Primer3 as the primer designing core algorithm. Locally stored sequence information and genomic variant information were hosted on MySQLv5.0 and were incorporated into RExPrimer.
resultsRExPrimer provides many functionalities for improved PCR primer design. Several databases, namely annotated human SNP databases, insertion/deletion (indel) polymorphisms database, pseudogene database, and structural genomic variation databases were integrated into RExPrimer, enabling an effective without-leaving-the-website validation of the resulting primers. By incorporating these databases, the primers reported by RExPrimer avoid mis-priming to related sequences (e.g. pseudogene, segmental duplication) as well as possible PCR failure because of structural polymorphisms (SNP, indel, and copy number variation (CNV)). To prevent mismatching caused by unexpected SNPs in the designed primers, in particular the 3' end (SNP-in-Primer), several SNP databases covering the broad range of population-specific SNP information are utilized to report SNPs present in the primer sequences. Population-specific SNP information also helps customize primer design for a specific population. Furthermore, RExPrimer offers a graphical user-friendly interface through the use of scalable vector graphic image that intuitively presents resulting primers along with the corresponding gene structure. In this study, we demonstrated the program effectiveness in successfully generating primers for strong homologous sequences.
conclusionThe improvements for primer design incorporated into RExPrimer were demonstrated to be effective in designing primers for challenging PCR experiments. Integration of SNP and structural variation databases allows for robust primer design for a variety of PCR applications, irrespective of the sequence complexity in the region of interest. This software is freely available at http://www4a.biotec.or.th/rexprimer.
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