What is CoSREM?
CoSREM (Combinatorial SRE Miner) is a graph mining algorithm to discover combinatorial SREs in human exons.
Requirements: This package is implemented under Python 3.3. and Centos 6. It was developped using PyDev.
Python packages to be intalled before use: networkx, matplotlib, and numpy.
1- Place the required data (input files are provided under the Data branch) in a specific directory.
Required files are:
hexmer-Ei-Order.csv : contains all possible 6-mers with their corresponding scores and ranks. exons+introns+new.csv : contains all unique coding exons for known human gene with thier flanking intronic regions. Exons1.txt : contains the first 50 nucleotides from the utilized exons
2- Create a folder called MCSs in the same directory.
3- Run CoSREM from terminal using this command:
python Main.py R Alpha Theta Path_to_directory where (R, Alpha, Theta, Path_to_directory) are user-defined parameters. R: the number of 6-mers with the highest ranks to be considere and the number of 6-mers with the lowest ranks as well. Alpha: the number of exons that two 6-mers should at least have in common to be considered one longer k-mer. Theta: the number of exons a set of SREs should at least have in common to be considered combinatorial SRE set. Path_to_directory: this is a string specifying the path to the input files.
4- After running CoSREM
The output files are:
1- All maximal cohesieve subgraphs will be created in the MCSs folder in gml format 2- attr.txt is a file that contains the attribues (shared exons IDs) of each maximal cohesive subgraph (MCS) ordered by the MCS IDs. 3- FinalSREs.txt includes the final result of all identified combinatorial SREs after the filtering stage.
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