The Perl software: -thermo_DR.pl:calculates the thermodynamic stability of DNA/RNA duplexes where RNA is identical to Crick strand -thermo_RD.pl:calculates the thermodynamic stability of RNA/DNA duplexes where RNA is identical to Watson strand -thermo_DD.pl:calculates the thermodynamic stability of DNA/DNA duplexes Calculations are carried out according to the nearest-neighbor method using a sliding window with arbitrary size and step. For all three Perl programs, 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: ./name of perl software, input file name, position of the nucleotide from which the calculation of ΔG will start,position of the nucleotide from which the calculation of ΔG will stop, window size, step size, >, the name of the output file. Example: ./thermo_DR.pl in.txt 50 6000 100 1 > out.txt In this case the sequence from In.txt will be calculated from 50nt to 6000nt with window size of 100bp and a step size of 1bp by thermo_DR.pl software. The result of this calculation will be saved in "out.txt" This should hopefully work with Mac :). If window size is an odd number, add 0.5 in the program where indicated. The equation for $G is: $G =$H*(1-310/($H/$S+18log[monovalent cation])): -Whan calculations are carried out in the presence of 10mM salt equation for $G is: $G =$H*(1-310/($H/$S-36)). The monovalent cation concentration is a default parameter of the program. -Whan calculations are carried out in the presence of 100mM salt the equation in the program has to be changed with: $G =$H*(1-310/($H/$S-18)) -Whan calculations are carried out in the presence of 1M salt the equation in the program has to be changed with: $G =$H*(1-310/($H/$S)) The thermodynamic parameters of the nearest-neighbor interactions for the DNA/DNA duplex are reported by Breslauer & Marky (1986)Proc Natl Acad Sci U S A, 83, 3746-3750. The thermodynamic parameters of the nearest-neighbor interactions for the RNA/DNA duplex are reported by Sugimoto and Co-authors (1995)Biochemistry, 34, 11211-11216 For each nucleotide couple "dNN" in the DNA Watson coding sequence "thermo_RD.pl" calculates delta G values for the nearest-neighbor interactions "rNN/dNN" in the RNA/DNA duplex (where RNA is identical to DNA Watson coding strand) using their [H, S] (see Fig.S2 in paper) 'dNN' =>"rNN/dNN" [H, S], 'dAA' => rAA/dTT [7.8, 0.0219], 'dTT' => rUU/dAA [11.5, 0.0364], 'dAT' => rAU/dTA [8.3, 0.0239], 'dTA' => rUA/dAT [7.8, 0.0232], 'dCA' => rCA/dGT [9.0, 0.0261], 'dTG' => rUG/dAC [10.4, 0.0284], 'dGT' => rGU/dCA [7.8, 0.0216], 'dAC' => rAC/dTG [5.9, 0.0123], 'dCT' => rCU/dGA [7.0, 0.0197], 'dAG' => rAG/dTC [9.1, 0.0235], 'dGA' => rGA/dCT [5.5, 0.0135], 'dTC' => rUC/dAG [8.6, 0.0229], 'dCG' => rCG/dGC [16.3, 0.0471], 'dGC' => rGC/dCG [8.0, 0.0171], 'dGG' => rGG/dCC [12.8, 0.0319], 'dCC' => rCC/dGG [9.3, 0.0232] For each nucleotide couple "dNN" in the DNA Watson coding sequence "thermo_DR.pl" calculates delta G values for the nearest-neighbor interactions "rNN/dNN" in the RNA/DNA duplex (where RNA is identical to Crick coding strand) using their [H, S],(see Fig.S2 in paper) 'dNN' =>"rNN/dNN" [H, S], 'dAA' => rUU/dAA [11.5, 0.0364], 'dTT' => rAA/dTT [7.8, 0.0219], 'dAT' => rUA/dAT [8.3, 0.0239], 'dTA' => rAU/dTA [7.8, 0.0232], 'dCA' => rUG/dAC [10.4, 0.0284], 'dTG' => rCA/dGT [9.0, 0.0261], 'dGT' => rAC/dTG [5.9, 0.0123], 'dAC' => rGU/dCA [7.8, 0.0216], 'dCT' => rAG/dTC [9.1, 0.0235], 'dAG' => rCU/dGA [7.0, 0.0197], 'dGA' => rUC/dAG [8.6, 0.0229], 'dTC' => rGA/dCT [5.5, 0.0135], 'dCG' => rGC/dCG [16.3, 0.0471], 'dGC' => rCG/dGC [8.0, 0.0171], 'dGG' => rCC/dGG [9.3, 0.0232], 'dCC' => rGG/dCC [12.8, 0.0319] The output file is .txt delimited and contains two columns: the first one indicates the position of the window (the positions of the 100bp windows are indicated as the position of their 51bp, of the 9bp windows- the position of their 5bp, of the 2bp windows -the position of their 2bp); the secon column is deltaG value of each window.