fill_Atract_params

Usage:
%seq = &fill_Atract_params( \%seq, \%Atract, \%Atract_3, \%Atract_5 );

Action:
This subroutine searches for both A and T tracts and fills in the appropriate parameters as supplied by the %Atract, %Atract_3 and %Atract_5 hashes. A "tract" is defined as a stretch of either A's or T's longer than or equal to $Atract{min} but less than or equal to $Atract{max} in length.

The parameters to use in filling in the tracts are user definable, set by the %Atract, %Atract_3 and %Atract_5 hashes. For example, the following definitions are standard values from Koo et al. 1990:

#####################################################
# Atract site parameter definitions
$Atract_tormod         = 2.4e-19; # torsional modulus (erg*cm)
$Atract_rpb            = 3.4e-8;  # rise/bp (cm)
$Atract_helical_repeat = 10.33;   # helical repeat (bp/360 degrees)

# Default Atract values for middle of Atract region
%Atract = (
    tilt       => 0,    
    roll       => 0,    
    twist      => 360/$Atract_helical_repeat,
    tilt_flex  => 4.842,
    roll_flex  => 4.842,
    twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod ) * 180/$PI,
    dz         => 3.4,
);
$Atract{min} = 4;       # minimum number of A's in Atract
$Atract{max} = 6;       # maximum number of A's in Atract

# Default Atract values for 5' junction of Atract
%Atract_5 = (
    tilt       => -7.7,
    roll       => 4.6,   
    twist      => 360/$Atract_helical_repeat,
    tilt_flex  => 4.842,
    roll_flex  => 4.842,
    twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
    dz         => 3.4,
);

# Default Atract values for 3' junction
%Atract_3 = (
    tilt       => 9.7,
    roll       => 0,
    twist      => 360/$Atract_helical_repeat,
    tilt_flex  => 4.842,
    roll_flex  => 4.842,
    twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
    dz         => 3.4,
);

Using these parameters, the following sequence.in file is generated for the Atract sequence: 5'-GCTAGCGAAAAATCGATC-3':

18
num       tilt    flex    roll    flex   twist    flex      dz
  1  G   0.000   4.842   0.000   4.842  34.450   4.388   3.400
  2  C   0.000   4.842   0.000   4.842  34.450   4.388   3.400
  3  T   0.000   4.842   0.000   4.842  34.450   4.388   3.400
  4  A   0.000   4.842   0.000   4.842  34.450   4.388   3.400
  5  G   0.000   4.842   0.000   4.842  34.850   4.388   3.400
  6  C   0.000   4.842   0.000   4.842  34.850   4.388   3.400
  7  G  -7.700   4.842   4.600   4.842  34.850   4.388   3.400
  8  A   0.000   4.842   0.000   4.842  34.850   4.388   3.400
  9  A   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 10  A   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 11  A   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 12  A   9.700   4.842   0.000   4.842  34.850   4.388   3.400
 13  T   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 14  C   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 15  G   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 16  A   0.000   4.842   0.000   4.842  34.450   4.388   3.400
 17  T   0.000   4.842   0.000   4.842  34.450   4.388   3.400
 18  C   0.000   4.842   0.000   4.842  34.450   4.388   3.400

Using these parameters, the following sequence.in file is generated for the complimentary Ttract sequence: 5'-GATCGATTTTTCGCTAGC-3':

18
num       tilt    flex    roll    flex   twist    flex      dz
  1  G   0.000   4.842   0.000   4.842  34.450   4.388   3.400
  2  A   0.000   4.842   0.000   4.842  34.450   4.388   3.400
  3  T   0.000   4.842   0.000   4.842  34.450   4.388   3.400
  4  C   0.000   4.842   0.000   4.842  34.850   4.388   3.400
  5  G   0.000   4.842   0.000   4.842  34.850   4.388   3.400
  6  A  -9.700   4.842   0.000   4.842  34.850   4.388   3.400
  7  T   0.000   4.842   0.000   4.842  34.850   4.388   3.400
  8  T   0.000   4.842   0.000   4.842  34.850   4.388   3.400
  9  T   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 10  T   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 11  T   7.700   4.842   4.600   4.842  34.850   4.388   3.400
 12  C   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 13  G   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 14  C   0.000   4.842   0.000   4.842  34.850   4.388   3.400
 15  T   0.000   4.842   0.000   4.842  34.450   4.388   3.400
 16  A   0.000   4.842   0.000   4.842  34.450   4.388   3.400
 17  G   0.000   4.842   0.000   4.842  34.450   4.388   3.400
 18  C   0.000   4.842   0.000   4.842  34.450   4.388   3.400

Notice that the tilt parameters are opposite sign between the Ttract and the Atract, while the roll parameter is the same sign. Remember, these sequences represent the SAME chain.