"

From 2013.igem.org

/**

*  DATA VALUES
*/

var amino_acids = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0};

// amino acid weights - http://web.expasy.org/findmod/findmod_masses.html#AA var amino_weights = { "A": 71.0788, "C": 103.1388, "D": 115.0886, "E": 129.1155, "F": 147.1766, "G": 57.0519, "H": 137.1411, "I": 113.1594, "K": 128.1741, "L": 113.1594, "M": 131.1926, "N": 114.1038, "P": 97.1167, "Q": 128.1307, "R": 156.1875, "S": 87.0782, "T": 101.1051, "V": 99.1326, "W": 186.2132, "Y": 163.1760 }; var water_weight = 18.01528; //average molecular weight of one molecule of water

// Kyte & Doolittle index of hydrophobicity var kd = { 'A': 1.8, 'R':-4.5, 'N':-3.5, 'D':-3.5, 'C': 2.5,

     'Q':-3.5, 'E':-3.5, 'G':-0.4, 'H':-3.2, 'I': 4.5,
     'L': 3.8, 'K':-3.9, 'M': 1.9, 'F': 2.8, 'P':-1.6,
     'S':-0.8, 'T':-0.7, 'W':-0.9, 'Y':-1.3, 'V': 4.2 };

// Flexibility // Normalized flexibility parameters (B-values), average (Vihinen et al., 1994) var Flex= { 'A': 0.984, 'C': 0.906, 'E': 1.094, 'D': 1.068,

      'G': 1.031, 'F': 0.915, 'I': 0.927, 'H': 0.950,
      'K': 1.102, 'M': 0.952, 'L': 0.935, 'N': 1.048,
      'Q': 1.037, 'P': 1.049, 'S': 1.046, 'R': 1.008,
      'T': 0.997, 'W': 0.904, 'V': 0.931, 'Y': 0.929};

// Hydrophilicity // 1 Hopp & Wood // Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). var hw = { 'A':-0.5, 'R': 3.0, 'N': 0.2, 'D': 3.0, 'C':-1.0,

     'Q': 0.2, 'E': 3.0, 'G': 0.0, 'H':-0.5, 'I':-1.8,
     'L':-1.8, 'K': 3.0, 'M':-1.3, 'F':-2.5, 'P': 0.0,
     'S': 0.3, 'T':-0.4, 'W':-3.4, 'Y':-2.3, 'V':-1.5 };

// Surface accessibility // 1 Emini Surface fractional probability var em = { 'A': 0.815, 'R': 1.475, 'N': 1.296, 'D': 1.283, 'C': 0.394,

     'Q': 1.348, 'E': 1.445, 'G': 0.714, 'H': 1.180, 'I': 0.603,
     'L': 0.603, 'K': 1.545, 'M': 0.714, 'F': 0.695, 'P': 1.236,
     'S': 1.115, 'T': 1.184, 'W': 0.808, 'Y': 1.089, 'V': 0.606 };

// 2 Janin Interior to surface transfer energy scale var ja = { 'A': 0.28, 'R':-1.14, 'N':-0.55, 'D':-0.52, 'C': 0.97,

     'Q':-0.69, 'E':-1.01, 'G': 0.43, 'H':-0.31, 'I': 0.60,
     'L': 0.60, 'K':-1.62, 'M': 0.43, 'F': 0.46, 'P':-0.42,
     'S':-0.19, 'T':-0.32, 'W': 0.29, 'Y':-0.15, 'V': 0.60 };

// A two dimentional dictionary for calculating the instability index. // Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990). // It is based on dipeptide values therefore the vale for the dipeptide DG is DIWV['D']['G']. var DIWV = { 'A': {'A': 1.0, 'C': 44.94, 'E': 1.0, 'D': -7.49,

             'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': -7.49,
             'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
             'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0 },
       'C': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 20.26,
             'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 33.60,
             'K': 1.0, 'M': 33.60, 'L': 20.26, 'N': 1.0,
             'Q': -6.54, 'P': 20.26, 'S': 1.0, 'R': 1.0,
             'T': 33.60, 'W': 24.68, 'V': -6.54, 'Y': 1.0},
       'E': {'A': 1.0, 'C': 44.94, 'E': 33.60, 'D': 20.26,
             'G': 1.0, 'F': 1.0, 'I': 20.26, 'H': -6.54,
             'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': 1.0,
             'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
       'D': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
             'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
             'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 1.0, 'P': 1.0, 'S': 20.26, 'R': -6.54,
             'T': -14.03, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
       'G': {'A': -7.49, 'C': 1.0, 'E': -6.54, 'D': 1.0,
             'G': 13.34, 'F': 1.0, 'I': -7.49, 'H': 1.0,
             'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': -7.49,
             'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
             'T': -7.49, 'W': 13.34, 'V': 1.0, 'Y': -7.49},
       'F': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 13.34,
             'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
             'K': -14.03, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
             'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 33.601},
       'I': {'A': 1.0, 'C': 1.0, 'E': 44.94, 'D': 1.0,
             'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 13.34,
             'K': -7.49, 'M': 1.0, 'L': 20.26, 'N': 1.0,
             'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
             'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
       'H': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
             'G': -9.37, 'F': -9.37, 'I': 44.94, 'H': 1.0,
             'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 24.68,
             'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
             'T': -6.54, 'W': -1.88, 'V': 1.0, 'Y': 44.94},
       'K': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
             'G': -7.49, 'F': 1.0, 'I': -7.49, 'H': 1.0,
             'K': 1.0, 'M': 33.60, 'L': -7.49, 'N': 1.0,
             'Q': 24.64, 'P': -6.54, 'S': 1.0, 'R': 33.60,
             'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
       'M': {'A': 13.34, 'C': 1.0, 'E': 1.0, 'D': 1.0,
             'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 58.28,
             'K': 1.0, 'M': -1.88, 'L': 1.0, 'N': 1.0,
             'Q': -6.54, 'P': 44.94, 'S': 44.94, 'R': -6.54,
             'T': -1.88, 'W': 1.0, 'V': 1.0, 'Y': 24.68},
       'L': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
             'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
             'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 33.60, 'P': 20.26, 'S': 1.0, 'R': 20.26,
             'T': 1.0, 'W': 24.68, 'V': 1.0, 'Y': 1.0},
       'N': {'A': 1.0, 'C': -1.88, 'E': 1.0, 'D': 1.0,
             'G': -14.03, 'F': -14.03, 'I': 44.94, 'H': 1.0,
             'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': -6.54, 'P': -1.88, 'S': 1.0, 'R': 1.0,
             'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 1.0},
       'Q': {'A': 1.0, 'C': -6.54, 'E': 20.26, 'D': 20.26,
             'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
             'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 1.0,
             'T': 1.0, 'W': 1.0, 'V': -6.54, 'Y': -6.54},
       'P': {'A': 20.26, 'C': -6.54, 'E': 18.38, 'D': -6.54,
             'G': 1.0, 'F': 20.26, 'I': 1.0, 'H': 1.0,
             'K': 1.0, 'M': -6.54, 'L': 1.0, 'N': 1.0,
             'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': -6.54,
             'T': 1.0, 'W': -1.88, 'V': 20.26, 'Y': 1.0},
       'S': {'A': 1.0, 'C': 33.60, 'E': 20.26, 'D': 1.0,
             'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
             'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 20.26, 'P': 44.94, 'S': 20.26, 'R': 20.26,
             'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
       'R': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
             'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 20.26,
             'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 13.34,
             'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 58.28,
             'T': 1.0, 'W': 58.28, 'V': 1.0, 'Y': -6.54},
       'T': {'A': 1.0, 'C': 1.0, 'E': 20.26, 'D': 1.0,
             'G': -7.49, 'F': 13.34, 'I': 1.0, 'H': 1.0,
             'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': -14.03,
             'Q': -6.54, 'P': 1.0, 'S': 1.0, 'R': 1.0,
             'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
       'W': {'A': -14.03, 'C': 1.0, 'E': 1.0, 'D': 1.0,
             'G': -9.37, 'F': 1.0, 'I': 1.0, 'H': 24.68,
             'K': 1.0, 'M': 24.68, 'L': 13.34, 'N': 13.34,
             'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
             'T': -14.03, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
       'V': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': -14.03,
             'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 1.0,
             'K': -1.88, 'M': 1.0, 'L': 1.0, 'N': 1.0,
             'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
             'T': -7.49, 'W': 1.0, 'V': 1.0, 'Y': -6.54},
       'Y': {'A': 24.68, 'C': 1.0, 'E': -6.54, 'D': 24.68,
             'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 13.34,
             'K': 1.0, 'M': 44.94, 'L': 1.0, 'N': 1.0,
             'Q': 1.0, 'P': 13.34, 'S': 1.0, 'R': -15.91,
             'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 13.34}
       };

// Data for the calculation of the Isoelectric Point /* pK values are from:

	* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,

J.-Ch., Frutiger, S. & Hochstrasser, D.F. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031. * Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539.

• /

var positive_pKs = {'Nterm': 7.5 , 'K': 10.0, 'R': 12.0, 'H': 5.98 }; var negative_pKs = {'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'C': 9.0 , 'Y': 10.0}; var pKcterminal = {'D': 4.55, 'E': 4.75}; var pKnterminal = {'A': 7.59, 'M': 7.0, 'S': 6.93, 'P': 8.36, 'T': 6.82, 'V': 7.44, 'E': 7.7}; var charged_aas = ['K', 'R', 'H', 'D', 'E', 'C', 'Y']; // or ProMost?

/**

*  FUNCTIONS
*/

function readSequence() { var sequence = document.getElementById("EnteredSequence").value; var cleanSequence = sequence.replace(/ /g, ""); return cleanSequence; };

function count_amino_acids(sequence){

   //Counts standard amino acids, returns an array {AminoAcid:Number}

var amino_acids_content = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0}; var amino_acids_freq = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0}; for (i=0; i<sequence.length; i++){ amino_acids_content[sequence[i]]++; } var total=sequence.length; for (aa in amino_acids){ amino_acids_freq[aa] = amino_acids_content[aa] * (100 / total); }; return [amino_acids_content,amino_acids_freq]; };

function compute_molecular_weight(amino_acids_content){ var molec_weight = water_weight; for (aa in amino_acids){ molec_weight = molec_weight + amino_acids_content[aa] * amino_weights[aa]; } return molec_weight; }

function findReadingFrame(sequence){ var a = 0; return a; }