Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009
  • Published Articles: 46

Full Length Research Paper

QPSOBT: One codon usage optimization software for protein heterologous expression

Yujie Cai1*, Jun Sun2, Jie Wang 2, Yanrui Ding2, Xiangru Liao1 and Wenbo Xu2
  1Key Laboratory of Industrial Biotechnology, School of Biotechnology, JiangNan University, 1800 Lihu road, Wuxi, Jiangsu 214122, China. 2School of Information Technology, JiangNan University, 1800 Lihu road, Wuxi, Jiangsu 214122, China.
Email: [email protected]

  •  Accepted: 17 May 2010
  •  Published: 30 June 2010

Abstract

 

QPSOBT is a codon usage optimization software based on the Quantum-behaved Particle Swarm Optimization (QPSO) algorithm. It can design synthetic genes of multikilobase sequences for protein heterologous expression rapidly. The program runs on .NET platform. Compared to the existing codon optimization software and web services, QPSOBT is able to generate better results when DNA/RNA sequence length is less than 6 kb which is a commonly-used range, especially when some restriction sites need to be removed. QPSOBT is freely available (www.sigcib.org/qpsobt.html).

 

Key words: Codon usage, quantum-behaved particle swarm, optimization, protein expression.