-ThermoNN.pl Perl software indicates nearest-neighbor interactions across the DNA-RNA duplexes  

The input file should be ".txt" and should contain the DNA sequence of the Watson coding strand (FASTA format). 
In order to run the program in the command line of the Terminal should be written:
./thermo_NN.pl input_file start_position stop_position 2 1 > output_file 
 
ThermoNN.pl indicates nearest-neighbor interactions across the DNA-RNA duplexes where RNA is equivalent to the Watson coding strand, using a sliding window with size 2 and step 1
 NN interactions are indicated by digits from 1 to 16 as follows:
rAA/dTT=1
rUU/dAA=2
rAU/dTA=3
rUA/dAT=4
rCA/dGT=5
rUG/dAC=6
rGU/dCA=7
rAC/dTG=8
rCU/dGA=9
rAG/dTC=10
rGA/dCT=11
rUC/dAG=12
rCG/dGC=13 
rGC/dCG=14
rGG/dCC=15
rCC/dGG=16
 

# output file is txt delimited file with two columns: the first one indicates the position of the second nucleotide in the nearest-neighbor(NN) couple; 
the second represents digits corresponding to particular NN interaction.