README

--------------- Installing GTModify ----------------
1. Download and extract GTModify.zip which gives a folder GTModify
2. Open terminal -> go to GTModify folder.
3. >>make
4. Code is now compiled.
5. Now run simply by typing ./GTModify everytime
 
Integrating GTModify with GTFold 
//Recommended but not required for below questions
1. Permanent way:
Open your ~/.bashrc file -> add the following line
>>export GTMODIFYRUNPATH=full path where the GTfold binary resides, for example in my computer it is:
>>export GTMODIFYRUNPATH=/home/abhishek/Desktop/gtfold/bin
2. Temporary way:
Simply type in your terminal
>>export GTMODIFYRUNPATH=full path where the GTfold binary resides

----------QUESTIONS to try out ----------------
Requirement: Each question should be (and can be) performed in a single query. 

Q1. Modify all internal 1x1 parameter values to contain 0
Q2. Modify all stack energies where closing Base Pair (cbp) can be anything and interior base pair is specified as 'ax'. Values should be made to -2.0
Q3. Modify internal 2x2 parameters, where closing base pair contains a 'c', interior base pair contains 'au' in any order, the unpaired bases should contain X1 = 'c', Y1 = 'g' and X2 and Y2 can be anything. Modify parameters to contain values from normal distribution with mean = 10 and std dev = 1
Q4. Modify terminal mismatch parameters for hairpin loops, where cbp should contain c,g in any order, and the terminal mismatch nucleotides can be anything. Values should be sampled from a uniform distribution with upper bound as 5.0 and lower bound as 1.
Q5. Modify internal 2x1 parameters where closing base pair is specified as 'gc' and the interior base pair and unpaired nucleotides can be anything. Values should be made as -1.5. 
Q6. Modify Dangle parameters with any closing base pair, and with X2 = a, values are displaced by -0.5
(Hint: read the prompt carefully, the usage for specifying X2 is slightly different as dangle parameters can either be X1 or X2 but never both) 

--------------------------------------

Jargon:

		X1	Y1	
5'-- 	B1			B11   -- 3'

3'-- 	B2			B22   -- 5'
		X2	Y2
	
B1, B2 denote closing base pairs, B11 B22 denote interior base pair(if applicable), X1 X2 Y1 Y2 denoted unpaired bases in the positions indicated(if applicable) 


Note: Usability & Specify Options:
1. When selecting any combination of bases, we can enter even less than 2 bases. That is if only 'a' is entered in this option say for closing bp, the algorithm matches all closing bp's which have an 'a' in them at any position.