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BMC Bioinformatics. 2015 Sep 21;16:303. doi: 10.1186/s12859-015-0743-5.

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

Author information

1
Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland. edward.daniel@oulu.fi.
2
Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland. goodluck.onwukwe@oulu.fi.
3
Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland. rik.wierenga@oulu.fi.
4
Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA. quaggin@northwestern.edu.
5
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. seppo.vainio@oulu.fi.
6
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. mirja.krause@oulu.fi.

Abstract

BACKGROUND:

Codon 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.

RESULTS:

We 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.

CONCLUSIONS:

This 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.

PMID:
26391121
PMCID:
PMC4578782
DOI:
10.1186/s12859-015-0743-5
[Indexed for MEDLINE]
Free PMC Article

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