kniekamp19 / mirandawebinterface Goto Github PK

~~ 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.