ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization

BMC Bioinformatics

Software

Goodluck U. Onwukwe¹  Rik K. Wierenga¹  Edward Daniel¹  Seppo J. Vainio²  Mirja Krause²  Susan E. Quaggin³ 

[1] Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland;Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5A, FIN-90220, Oulu, Finland;Feinberg School of Medicine, Northwestern University, 60611, Chicago, IL, USA;

关键词: Codon usage;    Sequence optimization;    Protein;    Translation;    DNA;   

DOI  :  10.1186/s12859-015-0743-5

 received in 2015-03-31, accepted in 2015-09-16,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundCodon usage plays a crucial role when recombinant proteins are expressed in different organisms. This is especially the case if the codon usage frequency of the organism of origin and the target host organism differ significantly, for example when a human gene is expressed in E. coli. Therefore, to enable or enhance efficient gene expression it is of great importance to identify rare codons in any given DNA sequence and subsequently mutate these to codons which are more frequently used in the expression host.ResultsWe describe an open-source web-based application, ATGme, which can in a first step identify rare and highly rare codons from most organisms, and secondly gives the user the possibility to optimize the sequence.ConclusionsThis application provides a simple user-friendly interface utilizing three optimization strategies: 1. one-click optimization, 2. bulk optimization (by codon-type), 3. individualized custom (codon-by-codon) optimization. ATGme is an open-source application which is freely available at: http://atgme.org

【 授权许可】

CC BY   
© Daniel et al. 2015