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

S. H. Chen, C. Y. Lin, C. S. Cho, C. Z. Lo, C. A. Hsiung

Research output: Contribution to journalArticlepeer-review

54 Citations (Scopus)


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

Original languageEnglish
Pages (from-to)3751-3754
Number of pages4
JournalNucleic Acids Research
Issue number13
Publication statusPublished - Jul 1 2003
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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