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

doi:10.1093/nar/gkg560

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 journal › Article › peer-review

54 Citations (Scopus)

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/.

Original language	English
Pages (from-to)	3751-3754
Number of pages	4
Journal	Nucleic Acids Research
Volume	31
Issue number	13
DOIs	https://doi.org/10.1093/nar/gkg560
Publication status	Published - Jul 1 2003
Externally published	Yes

ASJC Scopus subject areas

Genetics

Access to Document

10.1093/nar/gkg560

Cite this

@article{bde133a2f8514ea1bb1027c88cacabca,

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/.",

author = "Chen, {S. H.} and Lin, {C. Y.} and Cho, {C. S.} and Lo, {C. Z.} and Hsiung, {C. A.}",

year = "2003",

month = jul,

day = "1",

doi = "10.1093/nar/gkg560",

language = "English",

volume = "31",

pages = "3751--3754",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "13",

}

TY - JOUR

T1 - Primer Design Assistant (PDA)

T2 - A web-based primer design tool

AU - Chen, S. H.

AU - Lin, C. Y.

AU - Cho, C. S.

AU - Lo, C. Z.

AU - Hsiung, C. A.

PY - 2003/7/1

Y1 - 2003/7/1

N2 - 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/.

AB - 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/.

UR - http://www.scopus.com/inward/record.url?scp=0043122991&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0043122991&partnerID=8YFLogxK

U2 - 10.1093/nar/gkg560

DO - 10.1093/nar/gkg560

M3 - Article

C2 - 12824410

AN - SCOPUS:0043122991

SN - 0305-1048

VL - 31

SP - 3751

EP - 3754

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 13

ER -

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

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this