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| | Here is our team [https://igem.org/Team.cgi?id=535 roster] in the '''UNG server'''. | | Here is our team [https://igem.org/Team.cgi?id=535 roster] in the '''UNG server'''. |
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| - | #!/usr/bin/perl -w
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| - | use strict;
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| - | # prog1.1
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| - | # Bruno Contreras-Moreira
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| - | # Nearest Neighbor dG calculator
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| - |
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| - | # global variables
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| - | my $T = 37; # temperature(C)
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| - | my $windowL = 15; # window length, http://www.biomedcentral.com/1471-2105/6/1
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| - | my %NNparams = (
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| - | # SantaLucia J (1998) PNAS 95(4): 1460-1465.
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| - | # [NaCl] 1M, 37C & pH=7
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| - | # H(enthalpy): kcal/mol , S(entropy): cal/k·mol
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| - | # stacking dinucleotides
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| - | 'AA/TT' , {'H',-7.9, 'S',-22.2},
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| - | 'AT/TA' , {'H',-7.2, 'S',-20.4},
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| - | 'TA/AT' , {'H',-7.2, 'S',-21.3},
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| - | 'CA/GT' , {'H',-8.5, 'S',-22.7},
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| - | 'GT/CA' , {'H',-8.4, 'S',-22.4},
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| - | 'CT/GA' , {'H',-7.8, 'S',-21.0},
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| - | 'GA/CT' , {'H',-8.2, 'S',-22.2},
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| - | 'CG/GC' , {'H',-10.6,'S',-27.2},
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| - | 'GC/CG' , {'H',-9.8, 'S',-24.4},
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| - | 'GG/CC' , {'H',-8.0, 'S',-19.9},
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| - | # initiation costs
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| - | 'G' , {'H', 0.1, 'S',-2.8 },
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| - | 'A' , {'H', 2.3, 'S',4.1 },
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| - | # symmetry correction
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| - | 'sym' , {'H', 0, 'S',-1.4 } );
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| - |
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| - | #Se declaran los vectores donde se guardarán las secuencias cortadas en longitudes de 15 y 50.
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| - | my (@seq_win_50, @seq_win_100) = (0,0);
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| - | my ($start,$length,$a,$b,$D,$E1,$E2,$corazon) = (0,0,0,0,0,0,0,0);
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| - | my $seq = "GATTCGTCGCAGTGCGCTGCAATATAAAGTGCATTACGACACCACCCTGAACGGCGGCTTTGCCACCGCGATGGCGCTGAATGCCGATGCGACTGAAAAAGTAATTTCGGTGCAGGAAATGCACGCACAGATCAAATAATAGCGTGTCATGGCAGATATTTTTCATCCGCTAATTTGATCGAATAACTAATACGGTTCTCTGATGAGGACCGTTTTTTTTTGCCCATTAAGTAAATCTTTTGGGGAATCGATATTTTTGATGACATAAGCAGGATTTAGCTCACACTTATCGACGGTGAAGTTGCATACTATCGATATATCCACAATTTTAATATGGCCTTGTTTAATTGCTTCAAAACGAGTCATAGCCAGACTTTTAATTTGTGAAACTGGAGTTCGTATGTGTGAAGGATATGTTGAAAAACCACTCTACTTGTTAATCGCCGAATGG";
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| - |
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| - | #Hasta ahora el programa sólo separa las ventanas de tamaño 15 del primer set de 50 y 100 número de ventanas.
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| - | for(my $a=0; $a<50; $a++){
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| - | $start = $a;
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| - | $length = $windowL;
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| - | $seq_win_50[$a] = substr($seq,$start,$length);
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| - | }
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| - |
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| - | for(my $b=100; $b<200; $b++){
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| - | $start = $b;
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| - | $length = $windowL;
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| - | $seq_win_100[$b] = substr($seq,$start,$length);
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| - | }
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| - |
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| - | my$bug = duplex_deltaG($seq_win_50[0],$T,$windowL);
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| - | print $bug;
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| - | die;
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| - |
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| - | #Aquí en adelante ya no funciona...
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| - | for(my $n=0;$n<50;$n++){
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| - | $E1 += duplex_deltaG($seq_win_50[$n],$T,$windowL);
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| - | }
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| - | $E1 /= 50;
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| - |
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| - | for(my $m=0;$m<100;$m++){
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| - | $E2 += duplex_deltaG($seq_win_100[$m],$T,$windowL);
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| - | }
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| - | $E2 /= 100;
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| - |
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| - | $D = $E1 - $E2;
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| - | print $D;
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| - |
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| - | #Función de Bruno
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| - | sub duplex_deltaG
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| - | {
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| - | my ($seq,$tCelsius,$winsize) = @_;
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| - |
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| - | my ($DNAstep,$nt,$dG,$win_dG) = ('','',0,0);
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| - | my @sequence = split(//,uc($seq));
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| - | my $tK = 273.15 + $tCelsius;
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| - |
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| - | sub complement{ $_[0] =~ tr/ATGC/TACG/; return $_[0] }
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| - |
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| - | # add dG for overlapping dinculeotides
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| - | for(my $n=0;$n<=$winsize;$n++)
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| - | {
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| - | $DNAstep = $sequence[$n].$sequence[$n+1].'/'.
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| - | complement($sequence[$n].$sequence[$n+1]);
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| - |
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| - | if(!defined($NNparams{$DNAstep}))
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| - | {
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| - | $DNAstep = reverse($DNAstep);
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| - | }
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| - |
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| - | $dG = ((1000*$NNparams{$DNAstep}{'H'})-
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| - | ($tK*$NNparams{$DNAstep}{'S'}))
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| - | / 1000 ;
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| - |
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| - | $win_dG += $dG;
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| - | }
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| - |
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| - |
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| - | # add correction for helix initiation
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| - | $nt = $sequence[0]; # first pair
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| - | if(!defined($NNparams{$nt})){ $nt = complement($nt) }
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| - | $win_dG += ((1000*$NNparams{$nt}{'H'})-
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| - | ($tK*$NNparams{$nt}{'S'}))
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| - | / 1000;
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| - |
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| - | $nt = $sequence[$winsize]; # last pair
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| - | if(!defined($NNparams{$nt})){ $nt = complement($nt) }
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| - | $win_dG += ((1000*$NNparams{$nt}{'H'})-
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| - | ($tK*$NNparams{$nt}{'S'}))
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| - | / 1000;
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| - |
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| - | # please complete for symmetry correction
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| - |
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| - | return $win_dG;
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| - | }
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"
