title: Primer Design Assistant (PDA): A web-based primer design tool.
abstract: 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/.
authors.affiliation: Division of Biostatistics and Bioinformatics, National Health Research Institutes, 128, Yen-Chiu-Yuan Rd Sec. 2, Taipei 115, Taiwan.
authors.forename: S H
authors.initials: SH
authors.lastname: Chen
authors.forename: C Y
authors.initials: CY
authors.lastname: Lin
authors.forename: C S
authors.initials: CS
authors.lastname: Cho
authors.forename: C Z
authors.initials: CZ
authors.lastname: Lo
authors.forename: C A
authors.initials: CA
authors.lastname: Hsiung
mesh_terms: D017931:DNA Primers / Q000737:chemistry*; D019281:Dimerization; D020862:GC Rich Sequence; D020407:Internet; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers