ArticleBMC bioinformatics2015
ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 54 citations in OpenAlex.
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- A multiplexed, confinable CRISPR/Cas9 gene drive can propagate in caged Aedes aegypti populations.Nature communications · 2024Article
- Visual codon: a user-friendly Python program for viewing and optimizing gene GC content.PeerJ · 2024Article
- Codon-optimization in gene therapy: promises, prospects and challenges.Frontiers in bioengineering and biotechnology · 2024Review
- Expression and Functional Analysis of the Compact ThermophilicInternational journal of molecular sciences · 2023Article
- Purification and characterization of tomato arginine decarboxylase and its inhibition by the bacterial small molecule phevamine A.Protein expression and purification · 2023Article
- Refining theAnimals : an open access journal from MDPI · 2022Article
- Advances in COVID-19 mRNA vaccine development.Signal transduction and targeted therapy · 2022Review
- Traditional protocols and optimization methods lead to absent expression in a mycoplasma cell-free gene expression platform.Synthetic biology (Oxford, England) · 2022Article
- Increasing lipid yield in Yarrowia lipolytica through phosphoketolase and phosphotransacetylase expression in a phosphofructokinase deletion strain.Biotechnology for biofuels · 2021Article
- A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila.Genome biology · 2020Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.