Transgene-design: a web application for the design of mammalian transgenes.
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ABSTRACT: Summary
Transgene-design is a web application to help design transgenes for use in mammalian studies. It is predicated on the recent discovery that human intronless transgenes and native retrogenes can be expressed very effectively if the GC content at exonic synonymous sites is high. In addition, as exonic splice enhancers resident in intron containing genes may have different utility in intronless genes, these can be reduced or increased in density. Input can be a native gene or a commercially 'optimised' gene. The option to leave in the first intron and to protect or avoid other motifs is also permitted.Availability and implementation
Transgene-design is based on a ruby for rails platform. The application is available at https://transgene-design.bath.ac.uk. The code is available under GNU General Public License from GitHub (https://github.com/smuehlh/transgenes).Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Muhlhausen S
PROVIDER: S-EPMC9048660 | biostudies-literature | 2022 Apr
REPOSITORIES: biostudies-literature
Publications
Transgene-design: a web application for the design of mammalian transgenes.
Mühlhausen Stefanie S Hurst Laurence D LD
Bioinformatics (Oxford, England) 20220401 9
<h4>Summary</h4>Transgene-design is a web application to help design transgenes for use in mammalian studies. It is predicated on the recent discovery that human intronless transgenes and native retrogenes can be expressed very effectively if the GC content at exonic synonymous sites is high. In addition, as exonic splice enhancers resident in intron containing genes may have different utility in intronless genes, these can be reduced or increased in density. Input can be a native gene or a comm ...[more]
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