URPD: a specific product primer design tool

BMC Research Notes

Cheng-Hong Yang³  Yu-Huei Cheng¹  Li-Yeh Chuang² 

[1] Department of Digital Content Design and Management, Toko University, Chiayi, Taiwan;Department of Chemical Engineering, Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan;Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan

关键词: Virtual gel electrophoresis;    Genetic algorithm (GA);    Memetic algorithm (MA);    Web-based;    Primer design;    Polymerase chain reaction (PCR);   

Others  :  1166276
DOI  :  10.1186/1756-0500-5-306

 received in 2012-03-15, accepted in 2012-05-20,  发布年份 2012

【 摘 要 】

Background

Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users.

Findings

URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers.

Conclusions

URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/ webcite.

【 授权许可】

   
2012 Chuang et al.; licensee BioMed Central Ltd.

【 图 表 】

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