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PolDNAMelt

This program calculates the melting thermodynamics of a Contiguous polymeric ds-DNA in solution (with absolute base pairing complimentarity) spliting it into sizes of preferred window & overlap by the user

  • README
    •


  • REFERENCE
    •                  (pdf)
    STANDALONE VERSION (.tar.gz)
                    


  • Type a tag for your sequence :

    (optional)

  • Type your DNA sequence here :
    [ Max length :     8 kbp (without delimiters)]

    Enter the sense strand sequence
    (in 5` to 3` direction)
    Ensure to erase the comment written in the text box
    before you proceed to enter




    Base pair step parameters (Default : Santalucia)

        
        

  • Enter start bp position:

    default : +1

  • Enter Window Size (bp):

    default : 20 bp
    (For a shorter sequence, one must readjust accordingly)

  • Enter Overlap Size (bp):

    default : 0 bp

  • Enter Temperature (in degree Celcius):

    default : 37 (physiological)

  • Total Monovalent counterion concentration must be between 0.05 (M) and 1.1 (M)
    (Otherwise will forcefully be readjusted to the nearest cut off) :

  • Enter [Na+] concentration (in [Mols/Litre]) :

    default : 0.015 (physiological)

  • Enter [K+] concentration (in [Mols/Litre]) :

    default : 0.15 (physiological)

  • Enter [Tris+] concentration (in [Mols/Litre]) :

    default : 0.000

  • Enter [Mg++] concentration (in [Mols/Litre]) :

    default : 0.01
    (physiological range : 0.005 to 0.03 M
    among different cells)

    (For reliable Tm predictions,
    one should choose counterion concentrations
    near (or within) their physiological range)