title: EuGene: maximizing synthetic gene design for heterologous expression.
abstract: Numerous software applications exist to deal with synthetic gene design, granting the field of heterologous expression a significant support. However, their dispersion requires the access to different tools and online services in order to complete one single project. Analyzing codon usage, calculating codon adaptation index (CAI), aligning orthologs and optimizing genes are just a few examples. A software application, EuGene, was developed for the optimization of multiple gene synthetic design algorithms. In a seamless automatic form, EuGene calculates or retrieves genome data on codon usage (relative synonymous codon usage and CAI), codon context (CPS and codon pair bias), GC content, hidden stop codons, repetitions, deleterious sites, protein primary, secondary and tertiary structures, gene orthologs, species housekeeping genes, performs alignments and identifies genes and genomes. The main function of EuGene is analyzing and redesigning gene sequences using multi-objective optimization techniques that maximize the coding features of the resulting sequence.
  
  
  BACKGROUND
  EuGene is freely available for non-commercial use, at http://bioinformatics.ua.pt/eugene.
authors: DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. paulogaspar@ua.pt
authors: Paulo
authors: P
authors: Gaspar
authors: José Luís
authors: JL
authors: Oliveira
authors: Jörg
authors: J
authors: Frommlet
authors: Manuel A S
authors: MA
authors: Santos
authors: Gabriela
authors: G
authors: Moura
mesh_terms: D000465:Algorithms; D001482:Base Composition; D003062:Codon; D015870:Gene Expression; D005813:Genes, Synthetic; D016678:Genome; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D003062:Codon