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Web-based application for designing germline-optimized protein coding sequences for C. elegans
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dickinson-lab/germline
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SYSTEM REQUIREMENTS OPERATING SYSTEM Tested on Ubuntu 16.4.03 running nginx 1.10.3 web server Web application was tested using Google Chrome web browser on Mac OS X 10.12.6 DEPENDENCIES Perl 5.6.0 or higher (tested with version 5.22.1) Perl modules: BerkeleyDB (tested with version 0.55) BioPerl (tested with version 1.007002) CGI (tested with version 4.37) CGI::Application (tested with version 4.50) CGI::Application::Plugin::AutoRunmode (tested with version 0.18) CGI::Application::Plugin::Redirect (tested with version 1.00) CGI::Application::Plugin::Session (tested with version 1.05) Data::GUID (tested with version 0.049) HTML::Template (tested with version 2.97) JSON (tested with version 2.94) Math::Random (tested with version 0.72) PID::File (tested with version 0.32) POSIX (tested with version 1.53_01) Progress::Any (tested with version 0.20) Progress::Any::Output (tested with version 0.20) Progress::Any::Output::Callback (tested with version 0.04) Oracle BerkeleyDB (tested with version 5.3.28) INSTALLATION No installation required; to run the code, go to http://104.131.81.59/. DEMO Follow the instructions for use below. The contents of file GFP_S65C.fasta may be used as a test sequence with the “DNA sequence” option selected. INSTRUCTIONS FOR USE No data is required to run this code. To use the software: - Go to http://104.131.81.59/ - Enter a sequence name (optional) - Enter any DNA or Amino Acid sequence and select the appropriate option to specify which kind of sequence you entered - Check or uncheck the “add synthetic introns” box as desired - Click “Optimize” The program will generate and display a germline-optimized DNA sequence and its germline optimization score. If a DNA sequence was provided as input, the program will also display the germline optimization score of the input sequence. Expected run time varies depending on sequence length but should be 1-10 minutes for most sequences. Run time was 2.5 minutes for the GFP_S65C demo sequence.
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Web-based application for designing germline-optimized protein coding sequences for C. elegans
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