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View Code? Open in Web Editor NEWThis code generates a simple web interface for the miRNA target detection algorithm miRanda.
This code generates a simple web interface for the miRNA target detection algorithm miRanda.
~~ miRanda: micro RNA target detection web interface ~~ Kristen Niekamp AS.410.712.81.SP22: Advanced Practical Computer Concepts for Bioinformatics Webpage: http://bfx3.aap.jhu.edu/kniekam1/NiekampK_FinalProject/miranda.html Webpage must be accessed while on JHU network/VPN. This is a web interface for the miRanda miRNA target detection algorithm, which is currently available only as a command line program. It also makes use of Biocode's validate_fasta.py program to validate FASTA format in input files. miRanda local download: http://cbio.mskcc.org/miRNA2003/miranda.html. miRanda manpage: http://cbio.mskcc.org/microrna_data/manual.html **Note: miRanda must be installed in the same directory as run_miranda.cgi** Usage: To use the web interface, simply upload a FASTA-formatted file of miRNA sequences as the query and a FASTA-formatted file of genomic DNA sequences as the reference sequences. File sizes are currently limited to 100MB. The user may adjust parameters if so desired, but default parameters will suffice for most queries.The server will perform file validation and run the files through the miRanda algorithm. The results will appear as a table at the bottom of the page. Results are also stored in a MySQL database for later reference if needed. Example input files are located in the "examples" directory. Required Python packages: cgi; json; subprocess miRanda: Enright AJ, John B, Gaul U, Tuschl T, Sander C, and Marks DS. 2003. MicroRNA targets in Drosophila. Genome Biology 5(1):R1 The idea for this project came from the current lack of accessibility of many bioinformatics tools for researchers who are not trained in computer usage like command line practices or coding. In my undergraduate research, before I discovered my love for bioinformatics, I struggled immensely with having no training in using the command line and needing to be able to use certain tools in genomics research. Needing to use my university's high performance computer lead me to learning Linux command line usage, which uncovered the huge part of my field that I was missing out on. Making new tools and preexisting tools available for the average biology researcher is a passion of mine and my goal is to increase accessibility of bioinformatics analysis for future biologists.
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