title: ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization.
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.
authors.affiliation: Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland. edward.daniel@oulu.fi.
authors.forename: Edward
authors.initials: E
authors.lastname: Daniel
authors.affiliation: Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland. goodluck.onwukwe@oulu.fi.
authors.forename: Goodluck U
authors.initials: GU
authors.lastname: Onwukwe
authors.affiliation: Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland. rik.wierenga@oulu.fi.
authors.forename: Rik K
authors.initials: RK
authors.lastname: Wierenga
authors.affiliation: Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA. quaggin@northwestern.edu.
authors.forename: Susan E
authors.initials: SE
authors.lastname: Quaggin
authors.affiliation: 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.
authors.forename: Seppo J
authors.initials: SJ
authors.lastname: Vainio
authors.affiliation: 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.
authors.forename: Mirja
authors.initials: M
authors.lastname: Krause
mesh_terms: D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D004247:DNA / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D011994:Recombinant Proteins / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D003062:Codon; D011994:Recombinant Proteins; D004247:DNA