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PSO Algorithm for Primer Design

  • Ming-Hsien Lin
  • Yu-Huei Cheng
  • Cheng-San Yang
  • Hsueh-Wei Chang
  • Li-Yeh Chuang
  • Cheng-Hong Yang
Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 6)

In recent years, polymerase chain reactions (PCR) have been widely applied in medical science. The PCR technique allows a small amount of DNA to be amplified exponentially, thus ensuring that the amount of DNA is sufficient for DNA sequence analysis or gene therapy. It is important to choose a feasible primer pair to work quickly and efficiently.

Recently, many kinds of primer design software were developed, but most of these do not allow the use of sequence accession numbers for primer design. Examples are Primer Design Assistant (PDA) [4] and GeneFisher [8]. The system we introduce in this chapter is based on a particle swarm optimization (PSO) algorithm. It incorporates the RefSeq database, which enables users to enter sequence accession numbers directly, or to copy/paste entire sequences in order to design primer sets. The software interface allows users to easily design fitting primer sets according to their needs.

The user-friendly interface allows (1) accession number input, (2) sequence input, and (3) input of primer constraints. The proposed PSO algorithm helps in correctly and quickly identifying an optimal primer pair required for a specific PCR experiment. Finally, information about a feasible primer pair is graphically depicted on the user interface.

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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Ming-Hsien Lin
  • Yu-Huei Cheng
  • Cheng-San Yang
    • 1
  • Hsueh-Wei Chang
    • 2
  • Li-Yeh Chuang
    • 3
  • Cheng-Hong Yang
  1. 1.Hospital
  2. 2.Environmental BiologyKaohsiung
  3. 3.UniversityKaohsiung

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