README

A script for gene prediction based on comparison of results from three sources:
	http://genome.crg.es/geneid.html
	http://genes.mit.edu/GENSCAN.html
	http://exon.biology.gatech.edu/GeneMark/hmmchoice.html

The script selects the genes found by all methods and checks the prediction on the NCBI protein database.


To use scrip you should give execute permission to "run" file ( chmod +x run ).

run -h -s [file]
	-h help
	-s seqence_file (the same file that was used on searching genes pages:
			http://genome.crg.es/geneid.html
			http://genes.mit.edu/GENSCAN.html
			http://exon.biology.gatech.edu/GeneMark/hmmchoice.html )


	All result from sites listed above shoud be placed in the "files" folder (see "files/example").

	Result files are:
	-resut.csv: contains columns (separator is tab):
		WHICH_METHOD	+\-	WHERE_IS_START	WHERE_IS_STOP	Matching_in_other_methods

	-if some genes was found by all methods then in folder "result" you will find files generated by using blastx (nr database) on input seqence_file. 

	

	AUTHOR & OWNER: ALEKSANDER MUĆK


	Plans for the future: 
		-to add automatic method_result_file download from sites listed above.


You can see example by typing (where "example_seq" is file name given with script):
	run -s example_seq
after copying files from "files/example" to "files/".


IMORTANT!
The web_blast file was downloaded from: https://blast.ncbi.nlm.nih.gov/Blast.cgi