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Nucleic Acids Research, 2003, Vol. 31, No. 13 3751-3754
© 2003 Oxford University Press

Primer Design Assistant (PDA): a web-based primer design tool

S.H. Chen1, C.Y. Lin*, C.S. Cho, C.Z. Lo and C.A. Hsiung

Division of Biostatistics and Bioinformatics, National Health Research Institutes, #128, Yen-Chiu-Yuan Rd Sec. 2, Taipei 115, Taiwan 1 Institute of Zoology, National Taiwan University, Taipei, Taiwan

*To whom correspondence should be addressed. Tel: +886 226534401; Fax: +886 227890253; Email: cylin{at}nhri.org.tw
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux–Apache–MySQL–PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by built-in parameters setting. Advanced options on 5' GC content, 3' GC content, dimer check and hairpin check are available. The option of covered region constrains the PCR product to cover a user-defined segment. PDA accepts single sequence query or multiple ones in FASTA format. It produces optimal and homogenous primer pairs that meet the need in experimental design with large-scaled PCR amplifications. Considering the system loading, the size of a submitted sequence is limited to 10 kb and the total sequence number in a query is limited to 20. The authors may be contacted regarding other requirements for primer design. The web application can be found at http://dbb.nhri.org.tw/primer/.


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