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Profiles RNA structures and produces a summary graph in graphviz format
This project forked from gtdmmb/rnastructprofiling
Profiles RNA structures and produces a summary graph in graphviz format
RNAStructProfiling To download source code, click on "zip" link on the RNAStructProfiling github page (https://github.com/gtfold/RNAStructProfiling/zipball/master). To compile on a Unix/Linus machine, make sure the following files are in the same directory: --main.c --profile.h --profile.c --summaryGraph.c --summaryGraph.h --hashtbl.c --hashtbl.h --Makefile --graph.c --graph.h --memoryDFS.c --memoryDFS.h Open a terminal window, navigate to the directory that contains the above files, and type 'make' to compile the program. To run, you will need to input 1) a sequence file, and 2) an sfold 'sample_1000.out' file, or any other structure file that lists structures in triplet notation, with the delineation "Structure [number]" on a separate line before every structure. (Included in the github repository is a sequence file and a sample file from ecoli5S that may be used to run the program.) Usage (from within that same directory): ./RNAprofile [seq file] [sample file] [options] Common options: -v = verbose output that gives all helix classes and profiles with frequencies -h [percent] = filter out all helix classes that occur in less than [h] percent of the input sample structures -p [percent] = filter out all profiles that occur less than [p] percent of the input sample structures -g = disable graph making component of program (if only interested in helix and profile stats) -o [file name] = produces the output graphviz dot file called [file name]; 'profile.dot' used by default
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