Team:TU-Munich/AnnotatorCode2.js

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,I:0,H:0,K:0,L: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

// Extinction coefficients for Y(Tyr) and W(Trp), as well as Cystine (formed by disulfide bond of two Cysteine) var extinction = { Y:1490 , W:5500 , Cystine:125 };

//Kyte & Doolittle index of hydrophobicity // see http://www.sciencedirect.com/science/article/pii/0022283682905150 var k_d_hydrophobicity = { '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 };

//For the computation of the charge plot // following http://emboss.sourceforge.net/apps/release/6.5/emboss/apps/charge.html var emboss_charge = { 'A': 0, 'R':+1, 'N': 0, 'D': -1, 'C': 0, 'Q': 0, 'E':-1, 'G': 0, 'H':0.5, 'I': 0, 'L': 0, 'K':+1, 'M': 0, 'F': 0, 'P': 0, 'S': 0, 'T': 0, 'W': 0, 'Y': 0, 'V': 0 };


// 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}; // For some amino acids at the n-terminus the pK value is changed: var pKnterminal = {'A': 7.59, 'M': 7.0, 'S': 6.93, 'P': 8.36, 'T': 6.82, 'V': 7.44, 'E': 7.7}; //if one of these is N-terminal, this replaces the usual 7.5 for Nterm

var charged_aas = ['K', 'R', 'H', 'D', 'E', 'C', 'Y'];

var translation_table = { 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', 'TAA': '*', //STOP CODONS, shouldn't appear and already be removed 'TAG': '*', 'TGA': '*' };

var reverse_translation_table = { "A": ["GCT","GCC","GCA","GCG"], "C": ["TGT","TGC"], "D": ["GAT","GAC"], "E": ["GAA","GAG"], "F": ["TTT","TTC"], "G": ["GGT","GGC","GGA","GGG"], "H": ["CAT","CAC"], "I": ["ATT","ATC","ATA"], "K": ["AAA","AAG"], "L": ["TTA","TTG","CTT","CTC","CTA","CTG"], "M": ["ATG"], "N": ["AAT","AAC"], "P": ["CCT","CCC","CCA","CCG"], "Q": ["CAA","CAG"], "R": ["CGT","CGC","CGA","CGG","AGA","AGG"], "S": ["TCT","TCC","TCA","TCG","AGT","AGC"], "T": ["ACT","ACC","ACA","ACG"], "V": ["GTT","GTC","GTA","GTG"], "W": ["TGG"], "Y": ["TAT","TAC"] };

var stop_codons = {'TAA':0,'TAG':0, 'TGA' :0};

var non_synonymous_codons = { //these are excluded from the calculation of the CAI 'ATG':0, 'TGG':0 }; var non_synonymous_acids = { //these are ignored in the calculation of the tRNA usage 'M':0, 'W':0 };

var atomic_composition_of_aa = { // [ C , H , N , O , S ] // helpful: http://www.matrixscience.com/help/aa_help.html A: [3, 5,1,1,0], R: [6,12,4,1,0], N: [4, 6,2,2,0], D: [4, 5,1,3,0], C: [3, 5,1,1,1], Q: [5, 8,2,2,0], E: [5, 7,1,3,0], G: [2, 3,1,1,0], H: [6, 7,3,1,0], I: [6,11,1,1,0], L: [6,11,1,1,0], K: [6,12,2,1,0], M: [5, 9,1,1,1], F: [9, 9,1,1,0], P: [5, 7,1,1,0], S: [3, 5,1,2,0], T: [4, 7,1,2,0], W: [11,10,2,1,0], Y: [9, 9,1,2,0], V: [5, 9,1,1,0]};

// weights for the calculation of the CAI (codon adaptation index), see e.g. http://www.ihes.fr/~carbone/papers/Bioinformatics.pdf // method based on: Sharp,P.M. and Li,W-H. (1987) The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications var E_coli_codon_weights = { //from http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=37762&aa=1&style=N for E.coli & computing the weights for CAI calculation 'TTT': 1, 'TTC': 36/64, 'TTA': 18/38, 'TTG': 13/38, 'TCT': 18/20, 'TCC': 14/20, 'TCA': 18/20, 'TCG': 11/20, 'TAT': 1, 'TAC': 35/65, 'TGT': 1, 'TGC': 48/52, 'TGG': 1, 'CTT': 15/38, 'CTC': 10/38, 'CTA': 6/38, 'CTG': 1, 'CCT': 24/37, 'CCC': 16/37, 'CCA': 23/37, 'CCG': 1, 'CAT': 1, 'CAC': 37/63, 'CAA': 35/65, 'CAG': 1, 'CGT': 1, 'CGC': 26/30, 'CGA': 9/30, 'CGG': 15/30, 'ATT': 1, 'ATC': 31/47, 'ATA': 21/47, 'ATG': 1, 'ACT': 22/31, 'ACC': 1, 'ACA': 25/31, 'ACG': 22/31, 'AAT': 1, 'AAC': 41/59, 'AAA': 1, 'AAG': 29/71, 'AGT': 18/20, 'AGC': 1, 'AGA': 13/30, 'AGG': 7/30, 'GTT': 1, 'GTC': 19/32, 'GTA': 19/32, 'GTG': 29/32, 'GCT': 22/27, 'GCC': 26/27, 'GCA': 1, 'GCG': 25/27, 'GAT': 1, 'GAC': 35/65, 'GAA': 1, 'GAG': 36/64, 'GGT': 1, 'GGC': 29/34, 'GGA': 19/34, 'GGG': 18/34, 'TAA': 1, //STOP CODONS, shouldn't appear and already be removed 'TAG': 9/58, 'TGA': 33/58 };

var Mouse_codon_weights = { //from http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=10090&aa=1&style=N for mus musculus & computing the weights for CAI calculation 'TTT': 44/56, 'TTC': 1, 'TTA': 7/39, 'TTG': 13/39, 'TCT': 20/24, 'TCC': 22/24, 'TCA': 14/24, 'TCG': 5/24, 'TAT': 43/57, 'TAC': 1, 'TGT': 48/52, 'TGC': 1, 'TGG': 1, 'CTT': 13/39, 'CTC': 20/39, 'CTA': 8/39, 'CTG': 1, 'CCT': 1, 'CCC': 30/31, 'CCA': 29/31, 'CCG': 10/31, 'CAT': 41/59, 'CAC': 1, 'CAA': 26/74, 'CAG': 1, 'CGT': 8/22, 'CGC': 17/22, 'CGA': 12/22, 'CGG': 19/22, 'ATT': 34/50, 'ATC': 1, 'ATA': 16/50, 'ATG': 1, 'ACT': 25/35, 'ACC': 1, 'ACA': 29/35, 'ACG': 10/35, 'AAT': 43/57, 'AAC': 1, 'AAA': 39/61, 'AAG': 1, 'AGT': 15/24, 'AGC': 1, 'AGA': 1, 'AGG': 1, 'GTT': 17/46, 'GTC': 25/46, 'GTA': 12/46, 'GTG': 1, 'GCT': 29/38, 'GCC': 1, 'GCA': 23/38, 'GCG': 9/38, 'GAT': 45/55, 'GAC': 1, 'GAA': 41/59, 'GAG': 1, 'GGT': 18/33, 'GGC': 1, 'GGA': 26/33, 'GGG': 23/33, 'TAA': 28/49, //STOP CODONS, shouldn't appear and already be removed 'TAG': 23/49, 'TGA': 1 };

var Yeast_codon_weights = { //from http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4932&aa=1&style=N for Saccharomyces cerevisiae & computing the weights for CAI calculation 'TTT': 1, 'TTC': 41/59, 'TTA': 28/29, 'TTG': 1, 'TCT': 1, 'TCC': 16/26, 'TCA': 21/26, 'TCG': 10/26, 'TAT': 1, 'TAC': 44/56, 'TGT': 1, 'TGC': 37/63, 'TGG': 1, 'CTT': 13/29, 'CTC': 6/29, 'CTA': 14/29, 'CTG': 11/29, 'CCT': 31/42, 'CCC': 15/42, 'CCA': 1, 'CCG': 12/42, 'CAT': 1, 'CAC': 36/64, 'CAA': 1, 'CAG': 31/69, 'CGT': 14/48, 'CGC': 6/48, 'CGA': 7/48, 'CGG': 4/48, 'ATT': 1, 'ATC': 26/46, 'ATA': 27/46, 'ATG': 1, 'ACT': 1, 'ACC': 22/35, 'ACA': 30/35, 'ACG': 14/35, 'AAT': 1, 'AAC': 41/59, 'AAA': 1, 'AAG': 42/58, 'AGT': 16/26, 'AGC': 11/26, 'AGA': 1, 'AGG': 21/48, 'GTT': 1, 'GTC': 21/39, 'GTA': 21/39, 'GTG': 19/39, 'GCT': 1, 'GCC': 22/38, 'GCA': 29/38, 'GCG': 11/38, 'GAT': 1, 'GAC': 35/65, 'GAA': 1, 'GAG': 30/70, 'GGT': 1, 'GGC': 19/47, 'GGA': 22/47, 'GGG': 12/47, 'TAA': 1, //STOP CODONS, shouldn't appear and already be removed 'TAG': 23/47, 'TGA': 30/47 };

var Arabidopsis_codon_weights = { // from http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3702&aa=1&style=N 'TTT': 1, 'TTC': 49/51, 'TTA': 14/26, 'TTG': 22/26, 'TCT': 1, 'TCC': 13/28, 'TCA': 20/28, 'TCG': 10/28, 'TAT': 1, 'TAC': 48/52, 'TGT': 1, 'TGC': 40/60, 'TGG': 1, 'CTT': 1, 'CTC': 17/26, 'CTA': 11/26, 'CTG': 11/26, 'CCT': 1, 'CCC': 11/38, 'CCA': 33/38, 'CCG': 18/38, 'CAT': 1, 'CAC': 39/61, 'CAA': 1, 'CAG': 44/56, 'CGT': 17/35, 'CGC': 7/35, 'CGA': 12/35, 'CGG':9/35, 'ATT': 1, 'ATC': 35/41, 'ATA': 24/41, 'ATG': 1, 'ACT': 1, 'ACC': 20/34, 'ACA': 31/34, 'ACG': 15/34, 'AAT': 1, 'AAC': 48/52, 'AAA': 49/51, 'AAG': 1, 'AGT': 16/28, 'AGC': 13/28, 'AGA': 1, 'AGG': 20/35, 'GTT': 1, 'GTC': 19/40, 'GTA': 15/40, 'GTG': 26/40, 'GCT': 1, 'GCC': 16/43, 'GCA': 27/43, 'GCG': 14/43, 'GAT': 1, 'GAC': 32/68, 'GAA': 1, 'GAG': 48/52, 'GGT': 34/37, 'GGC': 14/37, 'GGA': 1, 'GGG': 16/37, 'TAA': 36/44, //STOP CODONS, shouldn't appear and already be removed 'TAG': 20/44, 'TGA': 1 };

var Subtilis_codon_weights = { //http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=1423&aa=1&style=N 'TTT': 1, 'TTC': 32/68, 'TTA': 21/24, 'TTG': 16/24, 'TCT': 20/23, 'TCC': 13/23, 'TCA': 1, 'TCG': 10/23, 'TAT': 1, 'TAC': 35/65, 'TGT': 46/54, 'TGC': 1, 'TGG': 1, 'CTT': 23/24, 'CTC': 11/24, 'CTA': 5/24, 'CTG': 1, 'CCT': 28/44, 'CCC': 9/44, 'CCA': 19/44, 'CCG': 1, 'CAT': 1, 'CAC': 32/68, 'CAA': 1, 'CAG': 48/52, 'CGT': 18/25, 'CGC': 20/25, 'CGA': 10/25, 'CGG': 17/25, 'ATT': 1, 'ATC': 37/49, 'ATA': 13/49, 'ATG': 1, 'ACT': 16/40, 'ACC': 17/40, 'ACA': 1, 'ACG': 27/40, 'AAT': 1, 'AAC': 44/56, 'AAA': 1, 'AAG': 30/70, 'AGT': 11/23, 'AGC': 1, 'AGA': 1, 'AGG': 10/25, 'GTT': 1, 'GTC': 26/28, 'GTA': 20/28, 'GTG': 26/28, 'GCT': 24/28, 'GCC': 22/28, 'GCA': 1, 'GCG': 26/28, 'GAT': 1, 'GAC': 36/64, 'GAA': 1, 'GAG': 32/68, 'GGT': 19/34, 'GGC': 1, 'GGA': 31/34, 'GGG': 16/34, 'TAA': 1, //STOP CODONS, shouldn't appear and already be removed 'TAG': 15/61, 'TGA': 24/61 };

var Physco_codon_weights = { //http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3218&aa=1&style=N 'TTT': 42/58, 'TTC': 1, 'TTA': 9/26, 'TTG': 1, 'TCT': 1, 'TCC': 16/20, 'TCA': 15/20, 'TCG': 17/20, 'TAT': 38/62, 'TAC': 1, 'TGT': 42/58, 'TGC': 1, 'TGG': 1, 'CTT': 18/26, 'CTC': 15/26, 'CTA': 8/26, 'CTG': 24/26, 'CCT': 1, 'CCC': 23/32, 'CCA': 25/32, 'CCG': 20/32, 'CAT': 49/51, 'CAC': 1, 'CAA': 43/57, 'CAG': 1, 'CGT': 14/19, 'CGC': 15/19, 'CGA': 17/19, 'CGG': 17/19, 'ATT': 41/43, 'ATC': 1, 'ATA': 16/43, 'ATG': 1, 'ACT': 1, 'ACC': 23/30, 'ACA': 24/30, 'ACG': 24/30, 'AAT': 47/53, 'AAC': 1, 'AAA': 35/65, 'AAG': 1, 'AGT': 14/20, 'AGC': 18/20, 'AGA': 17/19, 'AGG': 1, 'GTT': 25/43, 'GTC': 18/43, 'GTA': 13/43, 'GTG': 1, 'GCT': 1, 'GCC': 22/31, 'GCA': 25/31, 'GCG': 22/31, 'GAT': 1, 'GAC': 47/53, 'GAA': 39/61, 'GAG': 1, 'GGT': 25/30, 'GGC': 24/30, 'GGA': 1, 'GGG': 21/30, 'TAA': 27/37, //STOP CODONS, shouldn't appear and already be removed 'TAG': 1, 'TGA': 36/37 };


var list_of_features = { "TG":"RFC25 scar (shown in bold)", "RRRRR":"Arg5-tag", "AWRHPQFGG":"Strep-tag I", "WSHPQFEK":"Strep-tag II", "DYKDHDGDYKDHDIDYKDDDDK":"3xFlag-tag", "DYKDDDDK":"Flag-tag", "YPYDVPDYA":"HA-tag", "HHHHHH":"His6-tag", "HHHHH":"His5-tag", "EQKLISEEDL":"c-Myc-tag", "KETAAAKFERQHMDS":"S-tag", "KDHLIHNVHKEFHAHAHNK":"HAT-tag", "KRRWKKNFIAVSAANRFKKISSSGAL":"Calmodulin-binding-peptide", "TDKDMTITFTNKKDAE":"Isopep-tag", "AHIVMVDAYKPTK":"Spy-tag", "TNPGVSAWQVNTAYTAGQLVTYNGKTYKCLQPHTSLAGWEPSNVPALWQLQ":"Chitin-binding domain", "MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP":"SBP-tag", "GLNDIFEAQKIEWHE":"Avitag", "DDDDK":"Enterokinase cleavage site", "IDGR":"Factor Xa cleavage site", "IEGR":"Factor Xa cleavage site", "LVPRGS":"Thrombin cleavage site", "LEVLFQGP":"PreScission cleavage site", "ENLYFQG":"TEV cleavage site", "ETVRFQGS":"TVMV cleavage site" //Note: to extend this list also need to extend search_regexp below!!! };

var search_regexp = /(RRRRR|AWRHPQFGG|WSHPQFEK|DYKDHDGDYKDHDIDYKDDDDK|DYKDDDDK|YPYDVPDYA|HHHHHH|HHHHH|EQKLISEEDL|KETAAAKFERQHMDS|KDHLIHNVHKEFHAHAHNK|KRRWKKNFIAVSAANRFKKISSSGAL|TDKDMTITFTNKKDAE|AHIVMVDAYKPTK|TNPGVSAWQVNTAYTAGQLVTYNGKTYKCLQPHTSLAGWEPSNVPALWQLQ|MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP|GLNDIFEAQKIEWHE|DDDDK|IDGR|IEGR|LVPRGS|LEVLFQGP|ENLYFQG|ETVRFQGS)/g ;

/** 

*  FUNCTIONS
*/

//The function called initially. This handles interaction with the registry server to obtain the sequence function get_sequence(){ try{ //---put together the url from which to get the sequence var entered_bb_number = document.getElementById("EnteredBioBrick").value; var numeric_start = entered_bb_number.search(/[0-9]/); if (numeric_start == 0){ alert("Not a valid BioBrick name nor a nucleotide sequence. The BioBrick name must contain one letter followed by digits"); return; } if (numeric_start == -1){ //so entered a sequence //interpret the entered bb number as sequence bb_number = ""; //GLOBAL VARIABLE main_table_calc(entered_bb_number); } else{ //entered a BioBrick number, so try to get the sequence from the Registry bb_number = entered_bb_number.substr(numeric_start - 1); //GLOBAL VARIABLE bb_number = bb_number.toUpperCase(); var bb_url = "http://parts.igem.org/das/parts/dna/?segment=BBa_" + bb_number;

try{ jQuery.ajax({ url: bb_url, type: 'GET', success: function(res) { try{ var a = res.responseText; var b=a.indexOf("<body>");

var c=a.indexOf("

",b); var d=a.indexOf("

",c);

var obtained_sequence = a.substr(c+3,d-c-3); } catch(err){ var txt = "Couldn't get the sequence from the registry. The BioBrick does not exist in the data base."; txt = txt + "\n"; txt = txt + "\nPlease restart and enter the nucleotide sequence manually instead of the BioBrick number!"; alert(txt); return; //to end program

}

//---call the main function with the sequence information--- if (obtained_sequence == ""){ alert("The sequence obtained from the registry is empty.\nPlease restart and enter the sequence manually instead of the BioBrick number!"); return; //to end the program //sequence = prompt(prompttxt,""); //if couldn't get the sequence in this way, ask user to enter it manually } main_table_calc(obtained_sequence); } //end of the function called on success }); } catch(error){ alert(error); } } } catch(err){ txt="There was an error on this page in get_sequence().\n\n"; txt=txt + "Error description: \n" + err + "\n\n"; txt=txt + "Click OK to continue. \n\n"; alert(txt); }; }


//the main function, which calls the necessary functions to compute the table entries and puts the table together function main_table_calc(sequence) { try{ entered_nuc_sequence = clean_sequence(sequence); //GLOBAL VARIABLE reading_frame = find_reading_frame(entered_nuc_sequence); //GLOBAL VARIABLE reading_frame_start = reading_frame[0]; //the A in the ATG start codon //GLOBAL VARIABLE reading_frame_end = reading_frame[1]; //last nucleotide to be translated //GLOBAL VARIABLE //recall internal indexing starts at 0, external indexing at 1

entered_nuc_length = entered_nuc_sequence.length; //GLOBAL VARIABLE if (reading_frame_start == -9 && (reading_frame_end > entered_nuc_length - 1) ){ //so RFC25 coding_nuc_sequence = "ATGGCCGGC" + entered_nuc_sequence + "ACCGGT"; //add prefix and suffix //GLOBAL VARIABLE RFC_standard = "RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)"; //GLOBAL VARIABLE nuc_sequence_to_display_html = " " + "ATGGCCGGC" + entered_nuc_sequence.substr(0,9) + " ... " + entered_nuc_sequence.substr(entered_nuc_length-9) +"ACCGGT" ; //GLOBAL VARIABLE } else if ( reading_frame_end > entered_nuc_length - 1 ){ //stop codon in RFC10 suffix coding_nuc_sequence = entered_nuc_sequence.substr(reading_frame_start) + "TAC"; //GLOBAL VARIABLE RFC_standard = "RFC 10 using the stop codon in the suffix, so TAC was added (in italics) to the 3' end: (underlined part encodes the protein)"; //GLOBAL VARIABLE nuc_sequence_to_display_html = " " + entered_nuc_sequence.substr(0,reading_frame_start) + "" + entered_nuc_sequence.substr(reading_frame_start,9) + " ... " + entered_nuc_sequence.substr(entered_nuc_length-9) +"TAC" ; //GLOBAL VARIABLE } else { coding_nuc_sequence = entered_nuc_sequence.substr( reading_frame_start , reading_frame_end - reading_frame_start + 1); //GLOBAL VARIABLE RFC_standard = "RFC 10: (underlined part encodes the protein)"; //GLOBAL VARIABLE nuc_sequence_to_display_html = " " + entered_nuc_sequence.substr(0,reading_frame_start) + "" + entered_nuc_sequence.substr(reading_frame_start,9) + " ... " + entered_nuc_sequence.substr(reading_frame_end-8,9) +"" + entered_nuc_sequence.substr(reading_frame_end+1); //GLOBAL VARIABLE }

var trans_result = translate_to_aa_and_codon_count(coding_nuc_sequence); amino_sequence = trans_result[0]; //GLOBAL VARIABLE codon_count = trans_result[1]; //GLOBAL VARIABLE

md5sum = hex_md5(amino_sequence); //GLOBAL VARIABLE

/* //for test purposes, contains all sequence features (except RFC 25 scar) (as of 25/08/13) amino_sequence = "RRRRRGGAWRHPQFGGWSHPQFEKDYKDHDGDYKDHDIDYKDDDDKDYKDDDDKYPYDVPDYAHHHHHHEQKLISEEDLHHHHHKETAAAKFERQHMDSKDHLIHNVHKEFHAHAHNKKRRWKKNFIAVSAANRFKKISSSGAL" + "TDKDMTITFTNKKDAEAHIVMVDAYKPTKTNPGVSAWQVNTAYTAGQLVTYNGKTYKCLQPHTSLAGWEPSNVPALWQLQMDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPGLNDIFEAQKIEWHEDDDDK" + "IDGRIEGRLVPRGSLEVLFQGPENLYFQGETVRFQGS";

  • /

SequenceCollection = {}; //GLOBAL VARIABLE SequenceFeatures = find_sequence_features(coding_nuc_sequence,amino_sequence); //GLOBAL VARIABLE FeatureStarts = []; //GLOBAL VARIABLE FeatureEnds = []; //GLOBAL VARIABLE for (f in SequenceFeatures){ //f is in the start of the feature in the amino acid sequence starting from 1 var feat_start_num = parseInt(f); var feat_seq = SequenceFeatures[f]; // the aa sequence of the feature var feat_length = feat_seq.length; var feat_end_num = feat_start_num + feat_length - 1; //the last aa of the feature (starting from 1)

// Check for unwanted overlap information if ((feat_seq == "HHHHH") && (amino_sequence.substr(feat_start_num - 2, 6) == "HHHHHH")){ continue; //so is a His5-Tag and we already have the His6-Tag, so we skip it } if ((feat_seq == "HHHHHH") && (amino_sequence.substr(feat_start_num - 2, 6) == "HHHHHH")){ continue; //so is a His6-Tag overlapping with a previous His6-Tag, so we skip it } if ((feat_seq == "RRRRR") && (amino_sequence.substr(feat_start_num - 2, 5) == "RRRRR")){ continue; //so is a Arg5-Tag overlapping with a previous Arg5-Tag, so we skip it } if ((feat_seq == "DYKDDDDK") && (amino_sequence.substr(feat_start_num - 15, 22) == "DYKDHDGDYKDHDIDYKDDDDK")){ continue; //so is a Flag-Tag in a 3xFlag-Tag, so we skip it }

FeatureStarts.push(feat_start_num); //all the feature starts and features ends in amino acid sequence starting from 1 FeatureEnds.push(feat_end_num); //are collected in these arrays

if (SequenceCollection[list_of_features[SequenceFeatures[f]]]){ //so there already is something in the list SequenceCollection[list_of_features[SequenceFeatures[f]]].push(feat_start_num); SequenceCollection[list_of_features[SequenceFeatures[f]]].push(feat_end_num); } else{ SequenceCollection[list_of_features[SequenceFeatures[f]]] = [feat_start_num,feat_end_num] ; } }

var counting_result = count_amino_acids(amino_sequence); amino_content = counting_result[0]; //GLOBAL VARIABLE amino_freq = counting_result[1]; //GLOBAL VARIABLE total_aminos = amino_sequence.length; //GLOBAL VARIABLE

//GLOBAL VARIABLE codon_usage = analyze_codons(codon_count,amino_content); // 0 -> E_coli, 1 -> Yeast, 2 -> Mammalian, 3 -> Subtilis, 4 -> Arabidopsis, 5 -> Physco

var composition_results = compute_molecular_weight_and_atomic_composition(amino_content); molecular_weight = composition_results[0]; //GLOBAL VARIABLE atomic_composition = composition_results[1]; //GLOBAL VARIABLE

pI = compute_pI(amino_sequence,amino_content); //GLOBAL VARIABLE extinction_coeffs = compute_extinction_coeff(amino_content); //GLOBAL VARIABLE

hydrophobicity_charge_plot = compute_hydrophobicity_charge_plot(amino_sequence); //GLOBAL VARIABLE // array of arrays, in outer array 0 -> average hydrophobicity over window_size (5 for now) // in outer array 1 -> average charge over window_size (5 for now) // inner array is indexed by start of the different windows


call_rost_server(); // compile_output();

} catch(err){ txt="There was an error while computing the parameters.\n\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } alert(txt); return; //to end execution } };


function call_rost_server(){ try{ //compile addresses of the different queries url_localization = "http://rostlab.org/%7Eroos/get/lc2/?md5=" + md5sum; //Examples of md5sums in the database url_gene_ontology = "http://rostlab.org/%7Eroos/get/metastudent/?md5=" + md5sum; //c75924eebc204d66f8069fcfc3bf3514 url_alignments = "http://rostlab.org/%7Eroos/get/blastPsiRdb/?md5=" + md5sum; //7092948cd4a8ecb626e2612731a24912 url_disulfidbridge = "http://rostlab.org/%7Eroos/get/disulfinder/?md5=" + md5sum; url_transmembrane = "http://rostlab.org/%7Eroos/get/phdRdb/?md5=" + md5sum; url_sec_and_acc = "http://rostlab.org/%7Eroos/get/profRdb/?md5=" + md5sum; //SECondary structure and solvent ACCessibility $.when($.ajax( { url: url_localization, type: 'GET' } ), $.ajax( { url: url_gene_ontology, type: 'GET' } ), $.ajax( { url: url_alignments, type: 'GET' } ), $.ajax( { url: url_disulfidbridge, type: 'GET' } ), $.ajax( { url: url_transmembrane, type: 'GET' } ), $.ajax( { url: url_sec_and_acc, type: 'GET' } ) ).then(

//first in case of success of all ajax requests function( localization , gene_ontology , alignments , disulfidbridge , transmembrane , sec_and_acc ){ try{ /* The arguments (in the listed sequence) are arguments resolved for the first, second,... ajax requests, respectively. Each argument is an array with the following structure: [ data, statusText, jqXHR ] */ var localization_readout = localization[0]; var gene_ontology_readout = gene_ontology[0]; var alignments_readout = alignments[0]; var disulfidbridge_readout = disulfidbridge[0]; var transmembrane_readout = transmembrane[0]; var sec_and_acc_readout = sec_and_acc[0];


// 1. parse the localization results var loc_readout = (localization_readout.results).toString(); loc_readout = loc_readout.replace(/\s/g,""); loc_results = []; //GLOBAL VARIABLE

var loc_tabletag_pos = loc_readout.indexOf(""); if (loc_tabletag_pos == -1){ //so no results in the database for this sequence //maybe do something to calculate it loc_results = "no_data"; } else{ //so there is data in the database var a = loc_readout.indexOf("",loc_tabletag_pos + 9); //find the second row of the table var b = loc_readout.indexOf("</td><td>",a+1); var c = loc_readout.indexOf("</td><td>",b+1); var d = loc_readout.indexOf("</td><td>",c+1); var e = loc_readout.indexOf("</td><td>",d+1); var f = loc_readout.indexOf("</td><td>",e+1); var g = loc_readout.indexOf("</td><td>",f+1); var h = loc_readout.indexOf("</td>",g+1); loc_results[0] = loc_readout.substring(b+12,c-4); loc_results[1] = loc_readout.substring(c+12,d-4); loc_results[2] = loc_readout.substring(d+12,e-4); loc_results[3] = loc_readout.substring(e+12,f-4); loc_results[4] = loc_readout.substring(f+12,g-4); loc_results[5] = loc_readout.substring(g+12,h-4); } // end of localization results // 2. parse the gene ontology results var go_readout = (gene_ontology_readout.results).toString(); go_readout = go_readout.replace(/\s{2,}/g,""); //remove all occurences of multiple white space go_results = []; //GLOBAL VARIABLE var go_id_pos = go_readout.indexOf("<td/><td/>"); //this only appears in the case of no data if (go_id_pos == -1){ //so there are results var a = go_readout.indexOf("</tr><tr>"); //find the second row of the table var b = go_readout.indexOf("</td><td>",a+1); //find the second column there (MFO) var c = go_readout.indexOf("</td><td>",b+1); //find the third column (BPO) var d = go_readout.indexOf("</td></tr>",c+1); //the end of the third column var mfo_raw = go_readout.substring(b+12,c-4); var num_of_mfos = mfo_raw.length/16; var bpo_raw = go_readout.substring(c+12,d-4); var num_of_bpos = bpo_raw.length/16; var mfo_results = []; for ( j=0 ; j<num_of_mfos ; j++){ mfo_results.push([mfo_raw.substring(j*16,j*16+10),mfo_raw.substring(j*16+11,j*16+15)]); } mfo_results.sort(readout_result_sorter); //sort the results in descending order of mfo_results.splice(2); //only keep the top two results var bpo_results = []; for ( j=0 ; j<num_of_bpos ; j++){ bpo_results.push([bpo_raw.substring(j*16,j*16+10),bpo_raw.substring(j*16+11,j*16+15)]); } bpo_results.sort(readout_result_sorter); //sort the results in descending order of bpo_results.splice(2); //only keep the top two results go_results = [mfo_results,bpo_results]; } else{ //so no results in the database for this sequence //maybe do something to calculate them go_results="no_data"; } //end of gene ontology results // 3. parse the alignment results var ali_readout = (alignments_readout.results).toString(); ali_readout = ali_readout.replace(/\s{2,}/g,""); //remove all occurences of multiple white space ali_results = []; //GLOBAL VARIABLE var ali_validation = ali_readout.indexOf("#SEQLENGTH"); if (ali_validation > -1){ // so entry exists in data base var ali_search_regexp = /(pdb\|pdb\||sp\||tr\|)/g ; var matched_pdb_entries = []; var matched_sp_entries = []; var matched_tr_entries = []; var done_pdb_entries = {}; while ((match = ali_search_regexp.exec(ali_readout)) != null) { var a = ali_readout.indexOf(" ",match.index); // position of the first white space after the protein name var b = ali_readout.indexOf(" ",a+1); // position of the second white space after the protein name var c = ali_readout.indexOf(" ",b+1); // position of the third white space after the protein name if (match[0] == "pdb|pdb|"){ //so is a pdb entry var end_of_id = ali_readout.indexOf("_",match.index); var matched_prot_name = ali_readout.substring(match.index+8,end_of_id); if (matched_prot_name in done_pdb_entries){ //do nothing entry already exists } else{ done_pdb_entries[matched_prot_name]=" "; matched_pdb_entries.push( [matched_prot_name, ali_readout.substring(b+1,c)] ); } } else if (match[0] == "sp|"){ //so is a SwissProt entry var end_of_id = ali_readout.indexOf("|",match.index+4); var matched_prot_name = ali_readout.substring(match.index+3,end_of_id); matched_sp_entries.push([matched_prot_name, ali_readout.substring(b+1,c)] ); } else{ //so is a TrEMBL entry var end_of_id = ali_readout.indexOf("|",match.index+4); var matched_prot_name = ali_readout.substring(match.index+3,end_of_id); matched_tr_entries.push( [matched_prot_name, ali_readout.substring(b+1,c)] ); } } if (matched_pdb_entries.length > 0){ //avoid sorting empty array -> endless matched_pdb_entries.sort(readout_result_sorter(a, b)); } if (matched_sp_entries.length > 0){ //avoid sorting empty array -> endless matched_sp_entries.sort(readout_result_sorter(a, b)); } if (matched_tr_entries.length > 0){ //avoid sorting empty array -> endless matched_tr_entries.sort(readout_result_sorter(a, b)); } for ( j=2 ; j<matched_pdb_entries.length ; j++ ){ if( matched_pdb_entries[j][1] < 98 ){ //keep those which have a higher identity matched_pdb_entries.splice(j); break; } } for ( j=2 ; j<matched_sp_entries.length ; j++ ){ if( matched_sp_entries[j][1] < 98 ){ //keep those which have a higher identity matched_sp_entries.splice(j); break; } } for ( j=2 ; j<matched_tr_entries.length ; j++ ){ if( matched_tr_entries[j][1] < 98 ){ //keep those which have a higher identity matched_tr_entries.splice(j); break; } } ali_results= [ matched_sp_entries, matched_tr_entries, matched_pdb_entries ] ; //GLOBAL VARIABLE } else{ //so no results in the database for this sequence //maybe do something to calculate them ali_results="no_data"; } //end of alignment results // 4. parse the disulfid bridge prediction var dis_readout = (disulfidbridge_readout.results).toString(); dis_readout = dis_readout.replace(/\s{2,}/g,""); var dis_validation = dis_readout.indexOf("
"); dis_results = []; //GLOBAL VARIABLE if (dis_validation > -1){ var dis_search_regexp = /"#DB_bond">DB_bond</g ; while ((match = dis_search_regexp.exec(dis_readout)) != null) { var komma_pos = dis_readout.indexOf(",",match.index+27); var bracket_close_pos = dis_readout.indexOf(")",komma_pos); //alert(dis_readout.substring(match.index+27,komma_pos)); //alert(dis_readout.substring(komma_pos+1,bracket_close_pos)); dis_results.push([dis_readout.substring(match.index+27,komma_pos),dis_readout.substring(komma_pos+1,bracket_close_pos)]); } } else{ //so no results in the database for this sequence //maybe do something to calculate them dis_results = "no_data"; } //end of disulfid bridge prediction // 5. parse transmembrane results var trans_readout = (transmembrane_readout.results).toString(); trans_readout = trans_readout.replace(/\s{2,}/g,""); //remove excessive white space trans_results = []; //GLOBAL VARIABLE /* var NHTM_index = trans_readout.indexOf("# NHTM_BEST : "); var NHTM_end = trans_readout.indexOf(" (",NHTM_index); predicted_number_of_transmembrane_helices = trans_readout.substring(NHTM_index+14,NHTM_end); //GLOBAL VARIABLE */ var reliability_index = trans_readout.indexOf("# REL_BEST : "); if (reliability_index > -1){ var reliability_end = trans_readout.indexOf(" (",reliability_index); reliability_of_tm_prediction = trans_readout.substring(reliability_index+13,reliability_end); //GLOBAL VARIABLE var prhl = []; var pito = []; var b = trans_readout.indexOf("1S 1S 1S ",reliability_end); var a = b + 8; for ( j=0 ; j<total_aminos ; j++ ){ var a1 = trans_readout.indexOf(" ",a +1); //first space (between AA_number and AA) var a2 = trans_readout.indexOf(" ",a1+1); //... var a3 = trans_readout.indexOf(" ",a2+1); var a4 = trans_readout.indexOf(" ",a3+1); var a5 = trans_readout.indexOf(" ",a4+1); var a6 = trans_readout.indexOf(" ",a5+1); var a7 = trans_readout.indexOf(" ",a6+1); var a8 = trans_readout.indexOf(" ",a7+1); var a9 = trans_readout.indexOf(" ",a8+1); var a0 = trans_readout.indexOf(" ",a9+1); //tenth space var a = trans_readout.indexOf(" ",a0+1); //space between the lines of the table, i.e. seperates the AAs prhl.push(trans_readout.substr(a8+1,1)); pito.push(trans_readout.substr(a0+1,1)); } var counter = 0; var curr_pos = prhl[0]; var curr_conf = pito[0]; // i for inside, o for outside, T for transmembrane if (curr_pos=="H"){ var helix_start = 0; } while ( counter < total_aminos ){ if (curr_pos == "L"){ var helix_start = jQuery.inArray("H",prhl,counter+1); curr_pos = "H"; counter = helix_start; } else if (curr_pos == "H"){ var after_helix_end = jQuery.inArray("L",prhl,counter+1); if (after_helix_end == -1){ var helix_end = total_aminos; //so transmembrane till end } else{ var helix_end = after_helix_end - 1; } curr_pos = "L"; counter = after_helix_end; if (curr_conf == "i"){ var conf_description = "outwards"; var curr_conf = "o"; } else if (curr_conf == "o"){ var conf_description = "inwards"; var curr_conf = "i"; } else{ var end_conf = pito[counter]; if (end_conf == "o"){ var conf_description = "outwards"; } else if (end_conf == "i"){ var conf_description = "inwards"; } else{ var conf_description = "unknown"; } } trans_results.push([helix_start,helix_end,conf_description]); } else{ //DO SOMETHING FOR THIS CASE alert("bad data in database"); break; } if (counter == -1){ counter = total_aminos; //so terminate the while loop } } } else{ //so no results in the database for this sequence //maybe do something to calculate them trans_results = "no_data"; } //end of transmembrane prediction // 6. parse the secondary structure prediction var sec_readout = (sec_and_acc_readout.results).toString(); sec_readout = sec_readout.replace(/\s{2,}/g,""); var sec_validation = sec_readout.indexOf("Perl-RDB"); sec_results = []; //GLOBAL VARIABLE if (sec_validation > -1){ //so there's data var table_start = sec_readout.indexOf("Ot8 Ot9"); sec_readout = sec_readout.substr(table_start + 8); var sec = []; var acc = []; var sec_array = sec_readout.split(" "); for ( j=0 ; j<total_aminos ; j++ ){ sec.push(sec_array[j*30 + 3]); acc.push(sec_array[j*30 + 16]); } //SECondary structure output generation var sec_counter = 0; var sec_output = []; while ( sec_counter < total_aminos ){ var sec_start = sec[sec_counter]; if (sec_start == "E"){ var feat = "E"; var feat_start = sec_counter; } else if (sec_start == "H"){ var feat = "H"; var feat_start = sec_counter; } else{ var feat = "L"; } if (feat == "E"){ var aL = jQuery.inArray("L",sec,sec_counter); var aH = jQuery.inArray("H",sec,sec_counter); if (aL == -1){ aL = total_aminos; } if (aH == -1){ aH = total_aminos; } var feat_end = Math.min(aL-1,aH-1); sec_counter = feat_end + 1; sec_output.push(["E",feat_start,feat_end]); } else if (feat == "H"){ var aL = jQuery.inArray("L",sec,sec_counter); var aE = jQuery.inArray("E",sec,sec_counter); if (aL == -1){ aL = total_aminos; } if (aE == -1){ aE = total_aminos; } var feat_end = Math.min(aL-1,aE-1); sec_counter = feat_end + 1; sec_output.push(["H",feat_start,feat_end]); } else{ //so feat should be L, i.e. loop, which we don't care about var aE = jQuery.inArray("E",sec,sec_counter); var aH = jQuery.inArray("H",sec,sec_counter); if (aE == -1){ aE = total_aminos; } if (aH == -1){ aH = total_aminos; } var feat_end = Math.min(aE-1,aH-1); sec_counter = feat_end + 1; //do not care about this in the output } } //solvent ACCessability output generation var acc_counter = 0; var acc_output = []; while ( acc_counter < total_aminos ){ var acc_start = acc[acc_counter]; if (acc_start == "b"){ //b for buried var feat = "b"; var feat_start = acc_counter; } else if (acc_start == "e"){ //e for exposed var feat = "e"; var feat_start = acc_counter; } else{ var feat = "i"; //i for intermediate } if (feat == "b"){ var ai = jQuery.inArray("i",acc,acc_counter); var ae = jQuery.inArray("e",acc,acc_counter); if (ai == -1){ ai = total_aminos; } if (ae == -1){ ae = total_aminos; } var feat_end = Math.min(ae-1,ai-1); acc_counter = feat_end + 1; acc_output.push(["b",feat_start,feat_end]); } else if (feat == "e"){ var ai = jQuery.inArray("i",acc,acc_counter); var ab = jQuery.inArray("b",acc,acc_counter); if (ai == -1){ ai = total_aminos; } if (ab == -1){ ab = total_aminos; } var feat_end = Math.min(ab-1,ai-1); acc_counter = feat_end + 1; acc_output.push(["e",feat_start,feat_end]); } else{ //so feat should be i, i.e. intermediate, which we don't care about var ab = jQuery.inArray("b",acc,acc_counter); var ae = jQuery.inArray("e",acc,acc_counter); if (ab == -1){ ab = total_aminos; } if (ae == -1){ ae = total_aminos; } var feat_end = Math.min(ab-1,ae-1); acc_counter = feat_end + 1; //do not care about this in the output } } sec_results = [sec_output,acc_output]; } else{ //so no results in the database for this sequence //maybe do something to calculate them sec_results = "no_data"; } //end of SECondary structure and solvent ACCessability prediction compile_output(); } catch(err){ // ADD ERROR HANDLING, compile_output() WON'T THROW ANY ERRORS return; } } , //second in case of failure function(){ try{ alert("Couldn't connect to database, direct computations only"); loc_results = "no_data"; go_results = "no_data"; ali_results = "no_data"; dis_results = "no_data"; trans_results = "no_data"; sec_results = "no_data"; compile_output(); //declare elements without content OR put up a flag, which skips relevant parts of compile_output(); } catch(err){ // ADD ERROR HANDLING, compile_output() WON'T THROW ANY ERRORS return; } } ); } catch(err){ txt="There was an error while calling the database.\n\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } alert(txt); return; //to end execution } } function compile_output(){ try{ var SequenceFeatureTable = "
"; var number_of_features = 0; for (feature in SequenceCollection){ if ( SequenceCollection.hasOwnProperty(feature) ){ number_of_features ++; } SequenceFeatureTable = SequenceFeatureTable + ""; } if (number_of_features == 0){ //so no features, so write something, so it doesn't appear empty SequenceFeatureTable = SequenceFeatureTable + "";

}

SequenceFeatureTable = SequenceFeatureTable + "
" + feature + ": ";

for ( i=0 ; i<(SequenceCollection[feature].length /2) ; i++ ){ SequenceFeatureTable = SequenceFeatureTable + SequenceCollection[feature][(2*i)].toString() + " to " + SequenceCollection[feature][(2*i) + 1].toString(); if (i+1 < (SequenceCollection[feature].length /2)){ // so not last entry SequenceFeatureTable = SequenceFeatureTable + ", "; } }

SequenceFeatureTable = SequenceFeatureTable + "
None of the supported features appeared in the sequence
";

//now add underline/bold to amino_output var Feature_Markups = FeatureStarts.concat(FeatureEnds);

//sort function needed for the sort below to work properly function sortNumber(a,b) { return a - b; } Feature_Markups.sort(sortNumber); //sort it //determine in which lines there is some markup to be done var Feature_Markups_lines = []; for ( i=0 ; i < Feature_Markups.length ; i++){ Feature_Markups_lines.push(Math.floor((Feature_Markups[i] - 1)/100)); }

// -- Prepare the output for the amino acid sequence -- var output_amino_sequence = amino_sequence + "*"; // first break the aa sequence into lines of 100 AAs var amino_lines = []; for ( i=0 ; i < output_amino_sequence.length /100 ; i++){ amino_lines.push(output_amino_sequence.substr(i*100,100)); } // next add the mark-up to the lines var amino_output_lines = []; if (Feature_Markups.length == 0){ amino_output_lines = amino_lines; //so no markup needed } else{ // so there is markup to be added var current_feature_element = 0; var open_close_index = 0; var open_close_index_bold = 0; for ( var line = 0; line<amino_lines.length ; line++ ){ amino_output_lines[line] = "" ; var last_element_pos = 0; if (open_close_index>0){ // so have open underlines at the end of previous line, so must reopen them for ( j = 0 ; j < open_close_index ; j++){ amino_output_lines[line]=amino_output_lines[line] + ""; } } if (open_close_index_bold>0){ // so have open bolds at the end of previous line, so must reopen them for ( j = 0 ; j < open_close_index_bold ; j++){ amino_output_lines[line]=amino_output_lines[line] + ""; } } while (Feature_Markups_lines[current_feature_element] == line){ //loop over all markups in this line var curr_element_pos = Feature_Markups[current_feature_element]; var curr_element_pos_inline = curr_element_pos - 100*line - 1; if ( jQuery.inArray( curr_element_pos , FeatureStarts ) > -1 ){ if (SequenceFeatures[curr_element_pos] == "TG"){ //so scar, so bold amino_output_lines[line] = amino_output_lines[line] + amino_lines[line].substring(last_element_pos,curr_element_pos_inline) + "<b>"; open_close_index_bold ++; } else{ //so underline amino_output_lines[line] = amino_output_lines[line] + amino_lines[line].substring(last_element_pos,curr_element_pos_inline) + "<u>"; open_close_index ++; } last_element_pos = curr_element_pos_inline; FeatureStarts.shift(); //removes the element which was just marked } else if ( jQuery.inArray( curr_element_pos , FeatureEnds ) > -1 ){ if (SequenceFeatures[curr_element_pos-1] == "TG"){ //so scar, so bold amino_output_lines[line] = amino_output_lines[line] + amino_lines[line].substring(last_element_pos,curr_element_pos_inline+1) + ""; open_close_index_bold = open_close_index_bold - 1; } else{ //so underline amino_output_lines[line] = amino_output_lines[line] + amino_lines[line].substring(last_element_pos,curr_element_pos_inline+1) + ""; open_close_index = open_close_index - 1; } last_element_pos = curr_element_pos_inline+1; FeatureEnds.shift(); //removes the element which was just marked } current_feature_element++; //update so we get next markup } //add the remainder of the line to the output amino_output_lines[line] = amino_output_lines[line] + amino_lines[line].substr(last_element_pos); if (open_close_index>0){ //so have open underlines at the end of this line, so must close them for now for ( j = 0 ; j < open_close_index ; j++){ amino_output_lines[line]=amino_output_lines[line] + "</u>"; } } if (open_close_index_bold>0){ //so have open underlines at the end of this line, so must close them for now for ( j = 0 ; j < open_close_index_bold ; j++){ amino_output_lines[line]=amino_output_lines[line] + "</b>"; } } } } // create amino_output table with the mark up

var amino_output = ""; amino_output = amino_output + "
1 ";

for ( j=1 ; j<amino_lines.length ; j++ ){ amino_output = amino_output + "
" + (j*100 + 1).toString() + " "; }

amino_output = amino_output + "		";

for ( j=0 ; j<amino_lines.length-1 ; j++ ){ amino_output = amino_output + amino_output_lines[j] + "
"; } amino_output = amino_output + amino_output_lines[amino_lines.length - 1];

amino_output = amino_output + "
";

var atomic_composition_output = "C" + atomic_composition[0] + "H" + atomic_composition[1] + "N" + atomic_composition[2] + "O" + atomic_composition[3] + ""; if (atomic_composition[4] != 0){ //so there is S in the aa, so add it atomic_composition_output = atomic_composition_output + "S" + atomic_composition[4] + ""; }

//Interpret the codon_usage // 0 -> E_coli, 1 -> Yeast, 2 -> Mammalian, 3 -> Subtilis, 4 -> Arabidopsis, 5 -> Physco //translate numerical CAI values into categories: 1.00-0.80 -> excellent // 0.79-0.60 -> good // 0.59-0.40 -> acceptable // 0.39-0.20 -> bad // 0.19-0.00 -> very bad for (i=0;i<6;i++){ if (codon_usage[i] >= 0.80){ codon_usage[i] = "excellent (" + codon_usage[i].toFixed(2) + ")"; } else if (codon_usage[i] < 0.8 && codon_usage[i] >= 0.6){ codon_usage[i] = "good (" + codon_usage[i].toFixed(2) + ")"; } else if (codon_usage[i] < 0.6 && codon_usage[i] >= 0.4){ codon_usage[i] = "acceptable (" + codon_usage[i].toFixed(2) + ")"; } else if (codon_usage[i] < 0.4 && codon_usage[i] >= 0.2){ codon_usage[i] = "bad (" + codon_usage[i].toFixed(2) + ")"; } else{ codon_usage[i] = "very bad (" + codon_usage[i].toFixed(2) + ")"; } }


/* * CREATE PREDICTIONS OUTPUT */

PredictionTable = ""; //GLOBAL VARIABLE if (loc_results === "no_data" && go_results === "no_data" && ali_results === "no_data" && dis_results === "no_data" && trans_results === "no_data" && sec_results === "no_data" ){ //so no prediction results at all PredictionTable = "   There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.";

alert("There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours."); } else{

//localization output // loc_results; [loc in archaea,reliability,loc in bacteria,reliabilty,loc in eukariya,reliability] if (loc_results !== "no_data"){ PredictionTable = PredictionTable

+ ""

+ "Subcellular Localization (reliability in brackets)"

+ "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Archaea:" + loc_results[0] + " (" + loc_results[1] + "%)
Bacteria:" + loc_results[2] + " (" + loc_results[3] + "%)
Eukarya:" + loc_results[4] + " (" + loc_results[5] + "%)
" + ""; } else{ //no results PredictionTable = PredictionTable + ""

+ "Subcellular Localization (reliability in brackets)"

+ "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Archaea: -
Bacteria: -
Eukarya: -
" + ""; } //gene ontology output // go_results; [mfo, bpo]; mfo = [GO-number, reliability] if (go_results !== "no_data"){ var mfo_number = go_results[0].length; var bpo_number = go_results[1].length; if(mfo_number == 0){ var mfo_print_out = " - ";

} else if(mfo_number == 1){

var mfo_print_out = "<a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go_results[0][0][0] + "'>" + go_results[0][0][0] + "</a> (" + (go_results[0][0][1]*100).toFixed(0) + "%)" + "";

} else{

var mfo_print_out = "<a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go_results[0][0][0] + "'>" + go_results[0][0][0] + "</a> (" + (go_results[0][0][1]*100).toFixed(0) + "%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go_results[0][1][0] + "'>" + go_results[0][1][0] + "</a> (" + (go_results[0][1][1]*100).toFixed(0) + "%)" + "";

}

if(bpo_number == 0){

var bpo_print_out = " - ";

} else if(bpo_number == 1){

var bpo_print_out = "<a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go_results[1][0][0] + "'>" + go_results[1][0][0] + "</a> (" + (go_results[1][0][1]*100).toFixed(0) + "%)" + "";

} else{

var bpo_print_out = "<a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go_results[1][0][0] + "'>" + go_results[1][0][0] + "</a> (" + (go_results[1][0][1]*100).toFixed(0) + "%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go_results[1][1][0] + "'>" + go_results[1][1][0] + "</a> (" + (go_results[1][1][1]*100).toFixed(0) + "%)" + "";

}

PredictionTable = PredictionTable

+ "Gene Ontology (reliability in brackets)
" + "" + "" + "" + ""

+ mfo_print_out

+ "" + "" + ""

+ bpo_print_out

+ "" + "" + "" + "
Molecular Function Ontology:
Biological Process Ontology:
 
" + ""; } else{ //no results PredictionTable = PredictionTable + "Gene Ontology (reliability in brackets)
" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Molecular Function Ontology: -
Biological Process Ontology: -
 
" + ""; } //disulfidbridge and transmembrane output // dis_results; [start,end] // trans_results; [start,end,configuration] // reliability_of_tm_prediction; // (out of 100) var dis_list = ""; if (dis_results !== "no_data"){ if (dis_results.length === 0){ dis_list = dis_list + " - "; } else{ for ( j=0 ; j<dis_results.length ; j++){ dis_list = dis_list + dis_results[j][0].toString() + " to " + dis_results[j][1].toString(); if ( j < (dis_results.length - 1) ){ dis_list = dis_list + ", "; } } } } else{ //no results dis_list = dis_list + " - "; } PredictionTable = PredictionTable + "" + "Predicted features:" + "" + "" + "" + "
Disulfid bridges:" + dis_list + "
Transmembrane helices";


if (trans_results !== "no_data"){

PredictionTable = PredictionTable + " (reliability: " + ((reliability_of_tm_prediction*100).toFixed(0)).toString() + "%):		";

if (trans_results.length === 0){ PredictionTable = PredictionTable + " - "; } else{ for ( j=0 ; j<trans_results.length ; j++){ if (trans_results[j][2] !== "unknown"){ PredictionTable = PredictionTable + (trans_results[j][0]).toString() + " to " + (trans_results[j][1]).toString() + " going " + (trans_results[j][2]); } else{ PredictionTable = PredictionTable + (trans_results[j][0]).toString() + " to " + (trans_results[j][1]).toString(); }

if ( j < (trans_results.length - 1) ){ PredictionTable = PredictionTable + ", "; } } } } else{ //no results

PredictionTable = PredictionTable + ":		 - ";

}

PredictionTable = PredictionTable + "
";


//alingment output // ali_results; [sp, tr, pdb]; sp,tr,pdb=[identifier,identity out of 100] //TrEMBL: http://www.uniprot.org/uniprot/A6NI79 (where A6NI79 is the matched_prot_name) //PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=1i84 //SwissProt: http://www.uniprot.org/uniprot/A6NI79 (where A6NI79 is the matched_prot_name) if (ali_results !== "no_data"){

} else{ //no results

}

//SECondary structure and solvent ACCessability results // sec_results; [sec_output,acc_output]; sec_output = [type,start,end], acc_output = [type,start,end] if (sec_results !== "no_data"){

} else{ //no results

} } /* * END OF PREDICTIONS OUTPUT CREATION */


//Create the hydrophobicity & charge plot if (hydrophobicity_charge_plot == "sequence too short"){ //so no plot possible HydrophobicityChargePlot = "   The sequence is too short for a plot. It must be at least 5 nucleotides long."; HydrophobicityChargePlotScript = ""; } else{ hydrophobicity_datapoints = []; //GLOBAL VARIABLE charge_datapoints = []; //GLOBAL VARIABLE var hydrophobicity_datapoints_text = "["; var charge_datapoints_text = "[";

for ( j = 0 ; j<hydrophobicity_charge_plot[0].length ; j++ ){ hydrophobicity_datapoints.push([2.5+j,hydrophobicity_charge_plot[0][j]]); charge_datapoints.push([2.5+j,hydrophobicity_charge_plot[1][j]]); hydrophobicity_datapoints_text = hydrophobicity_datapoints_text + "[" + (2.5+j) + "," + hydrophobicity_charge_plot[0][j].toFixed(2) + "]"; if ( j + 1 == hydrophobicity_charge_plot[0].length){ hydrophobicity_datapoints_text = hydrophobicity_datapoints_text + "]"; } else{ hydrophobicity_datapoints_text = hydrophobicity_datapoints_text + ","; } charge_datapoints_text = charge_datapoints_text + "[" + (2.5+j) + "," + hydrophobicity_charge_plot[1][j].toFixed(2) + "]"; if ( j + 1 == hydrophobicity_charge_plot[0].length){ charge_datapoints_text = charge_datapoints_text + "]"; } else{ charge_datapoints_text = charge_datapoints_text + ","; } }

flot_plot_options = []; //GLOBAL VARIABLE flot_plot_options[0] = { grid: { //backgroundColor: { colors: [ '#fff', '#eee' ] }, borderWidth: { top: 0, right: 0, bottom: 0, left: 0 } }, legend: {show: false}, xaxes: [{ min: 0, max: 200, ticks: [[0.5, '1'], [24.5, '25'], [49.5, '50'], [74.5, '75'], [99.5, '100'], [124.5, '125'], [149.5, '150'], [174.5, '175'], [199.5, '200']], tickLength: -5 }], yaxes: [{ ticks: [[0, '0'], [4.5,'hydro-
phobic  '], [-4.5,'hydro-
philic  ']], min: -4.5, max: +4.5, font: { size: 12, lineHeight: 14, style: "italic", weight: "bold", family: "sans-serif", variant: "small-caps", color: 'rgba(100,149,237,1)' } }, { ticks: [[0, ], [1,'positive
 charge'], [-1,'negative
 charge']], position: 'right', min: -1, max: 1, font: { size: 12, lineHeight: 14, style: "italic", weight: "bold", family: "sans-serif", variant: "small-caps", color: 'rgba(255,99,71,1)' } }] }; number_of_plots = Math.ceil(amino_sequence.length/200); //GLOBAL VARIABLE

HydrophobicityChargePlot = " <input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot()' value='Show'>
"

+ "
";

for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){

HydrophobicityChargePlot = HydrophobicityChargePlot + "
";

flot_plot_options[plot_num] = $.extend(true, {} ,flot_plot_options[0]); flot_plot_options[plot_num].xaxes = [{ min: plot_num*200, max: (plot_num + 1)*200, ticks: [ [plot_num*200 + 0.5, (plot_num*200 + 1).toString()], [plot_num*200 + 24.5, (plot_num*200 + 25).toString()], [plot_num*200 + 49.5, (plot_num*200 + 50).toString()], [plot_num*200 + 74.5, (plot_num*200 + 75).toString()], [plot_num*200 + 99.5, (plot_num*200 + 100).toString()], [plot_num*200 + 124.5, (plot_num*200 + 125).toString()], [plot_num*200 + 149.5, (plot_num*200 + 150).toString()], [plot_num*200 + 174.5, (plot_num*200 + 175).toString()], [plot_num*200 + 199.5, (plot_num*200 + 200).toString()] ], tickLength: -5 }]; }

HydrophobicityChargePlot = HydrophobicityChargePlot + "
";

HydrophobicityChargePlotScript = "" + "" + "<script type='text/javascript' src='http://code.jquery.com/jquery-1.10.0.min.js'></script>" + "<script type='text/javascript' src='https://2013.igem.org/Team:TU-Munich/Flot.js?action=raw&ctype=text/js'></script>" + "<script>" + "var hydrophobicity_datapoints = " + hydrophobicity_datapoints_text + ";" + "var charge_datapoints = " + charge_datapoints_text + ";" + "var flot_plot_options = []; " + "flot_plot_options[0] = {" + "grid: {" + "borderWidth: {" + "top: 0," + "right: 0," + "bottom: 0," + "left: 0" + "}" + "}," + "legend: {show: false}," + "xaxes: [{" + "min: 0," + "max: 200," + "ticks: [[0.5, '1'], [24.5, '25'], [49.5, '50'], [74.5, '75'], [99.5, '100'], [124.5, '125'], [149.5, '150'], [174.5, '175'], [199.5, '200']]," + "tickLength: -5" + "}]," + "yaxes: [{" + "ticks: [[0, '0'], [4.5,'hydro-
phobic  '], [-4.5,'hydro-
philic  ']]," + "min: -4.5," + "max: +4.5," + "font: {" + "size: 12," + "lineHeight: 14," + "style: 'italic'," + "weight: 'bold'," + "family: 'sans-serif'," + "variant: 'small-caps'," + "color: 'rgba(100,149,237,1)'" + "}" + "}," + "{" + "ticks: [[0, ], [1,'positive
 charge'], [-1,'negative
 charge']]," + "position: 'right'," + "min: -1," + "max: 1," + "font: {" + "size: 12," + "lineHeight: 14," + "style: 'italic'," + "weight: 'bold'," + "family: 'sans-serif'," + "variant: 'small-caps'," + "color: 'rgba(255,99,71,1)'" + "}" + "}]" + "};" + "var number_of_plots = " + number_of_plots + ";" + "for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){" + "flot_plot_options[plot_num] = $.extend(true, {} ,flot_plot_options[0]);" + "flot_plot_options[plot_num].xaxes = [{" + "min: plot_num*200," + "max: (plot_num + 1)*200," + "ticks: [ [plot_num*200 + 0.5, (plot_num*200 + 1).toString()], " + "[plot_num*200 + 24.5, (plot_num*200 + 25).toString()], " + "[plot_num*200 + 49.5, (plot_num*200 + 50).toString()], " + "[plot_num*200 + 74.5, (plot_num*200 + 75).toString()], " + "[plot_num*200 + 99.5, (plot_num*200 + 100).toString()], " + "[plot_num*200 + 124.5, (plot_num*200 + 125).toString()], " + "[plot_num*200 + 149.5, (plot_num*200 + 150).toString()], " + "[plot_num*200 + 174.5, (plot_num*200 + 175).toString()], " + "[plot_num*200 + 199.5, (plot_num*200 + 200).toString()] ]," + "tickLength: -5" + "}];" + "};" + "function show_or_hide_plot(){" + "try {" + "if( $('#hydrophobicity_charge_button').val() =='Show' ){" + "$('#hydrophobicity_charge_container').css('display','block');" + "for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){" + "$.plot('#hydrophobicity_charge_placeholder'+ plot_num.toString()," + "[{ " + "color: 'rgba(100,149,237,1)'," + "data: hydrophobicity_datapoints," + "label: 'Hydrophobicity'," + "lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' }," + "yaxis: 1" + "}, {" + "color: 'rgba(255,99,71,1)'," + "data: charge_datapoints," + "label: 'Charge'," + "lines: { show: true, fill: true, fillColor: 'rgba(255,99,71,0.1)' }," + "yaxis: 2" + "}]," + "flot_plot_options[plot_num] );" + "}" + "$('#hydrophobicity_charge_button').val('Hide');" + "$('#hydrophobicity_charge_explanation').html('
Moving average over 5 amino acids for hydrophobicity (blue) and charge (red)');" + "}" + "else{" + "$('#hydrophobicity_charge_container').css('display','none');" + "$('#hydrophobicity_charge_button').val('Show');" + "$('#hydrophobicity_charge_explanation').html();" + "}" + "}" + "catch(err){" + "txt='There was an error with the button controlling the visibility of the plot.
';" + "txt=txt+'The originating error is:
' + err + '

';" + "alert(txt);" + "}" + "}" + "</script>";

};

var creation_time = new Date(); //time stamp

if (bb_number == ""){ var bb_number_appear = ""; } else{ var bb_number_appear = bb_number; }

// --- Create the output --- var htmlCode = "";

// Code to display the table htmlCode = htmlCode + "" + "<style type=\"text/css\">" + "table#AutoAnnotator {border:1px solid black; width:100%; border-collapse:collapse;} " + "th#AutoAnnotatorHeader { border:1px solid black; width:100%; background-color: rgb(221, 221, 221);} " //soll STRONG sein + "td.AutoAnnotator1col { width:100%; border:1px solid black; } " + "span.AutoAnnotatorSequence { font-family:'Courier New', Arial; } " + "td.AutoAnnotatorSeqNum { text-align:right; width:2%; } " + "td.AutoAnnotatorSeqSeq { width:98% } " + "td.AutoAnnotatorSeqFeat1 { width:3% } " + "td.AutoAnnotatorSeqFeat2a { width:27% } " + "td.AutoAnnotatorSeqFeat2b { width:97% } " + "td.AutoAnnotatorSeqFeat3 { width:70% } " + "table.AutoAnnotatorNoBorder { border:0px; width:100%; border-collapse:collapse; } " + "table.AutoAnnotatorWithBorder { border:1px solid black; width:100%; border-collapse:collapse; } " + "td.AutoAnnotatorOuterAmino { border:0px solid black; width:20% } " + "td.AutoAnnotatorInnerAmino { border:1px solid black; width:50% } " + "td.AutoAnnotatorAminoCountingOuter { border:1px solid black; width:40%; } " + "td.AutoAnnotatorBiochemParOuter { border:1px solid black; width:60%; } " + "td.AutoAnnotatorAminoCountingInner1 { width: 7.5% } " + "td.AutoAnnotatorAminoCountingInner2 { width:62.5% } " + "td.AutoAnnotatorAminoCountingInner3 { width:30% } " + "td.AutoAnnotatorBiochemParInner1 { width: 5% } " + "td.AutoAnnotatorBiochemParInner2 { width:55% } " + "td.AutoAnnotatorBiochemParInner3 { width:40% } " + "td.AutoAnnotatorCodonUsage1 { width: 3% } " + "td.AutoAnnotatorCodonUsage2 { width:14.2% } " + "td.AutoAnnotatorCodonUsage3 { width:13.8% } " + "td.AutoAnnotatorLocalizationOuter {border:1px solid black; width:40%} " + "td.AutoAnnotatorGOOuter {border:1px solid black; width:60%} " + "td.AutoAnnotatorLocalization1 { width: 7.5% } " + "td.AutoAnnotatorLocalization2 { width: 22.5% } " + "td.AutoAnnotatorLocalization3 { width: 70% } " + "td.AutoAnnotatorGO1 { width: 5% } " + "td.AutoAnnotatorGO2 { width: 35% } " + "td.AutoAnnotatorGO3 { width: 60% } " + "td.AutoAnnotatorPredFeat1 { width:3% } " + "td.AutoAnnotatorPredFeat2a { width:27% } " + "td.AutoAnnotatorPredFeat3 { width:70% } "


// table.class //für Klassen + "</style>"

+ "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" // close the cell of Amino acid composition + "" + "" //close Amino acid counting cell + "" //close Biochemical parameters cell + "" + "" + "" + "" //close Codon usage cell + "" + "" + "" + PredictionTable + "" + "" + "
Protein data table for BioBrick <a href=\"http://parts.igem.org/wiki/index.php?title=Part:BBa_" + bb_number_appear + "\">BBa_" + bb_number_appear + "</a> automatically created by the <a href=\"https://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator\">BioBrick-AutoAnnotator</a> version 1.0" + "
" + "Nucleotide sequence in " + RFC_standard + "
" + nuc_sequence_to_display_html + "" + "
" + " ORF from nucleotide position " + (reading_frame_start + 1) + " to " + (reading_frame_end + 1) + " (excluding stop-codon)" + "
Amino acid sequence: (RFC25 scars in shown in bold, other sequence features underlined; both given below)
" + amino_output + "
Sequence features: (with their position in the amino acid sequence, see the <a href=\"https://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList\">list of supported features</a>)"

+ SequenceFeatureTable //created above

+ "
Amino acid composition:"

//TABLE IN TABLE

+ "" + "" + "" + "" + "" + "" + "" + "" + "
" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Ala (A)" + "" + amino_content.A + " (" + amino_freq.A.toFixed(1) + "%)" + "
Arg (R)" + "" + amino_content.R + " (" + amino_freq.R.toFixed(1) + "%)" + "
Asn (N)" + "" + amino_content.N + " (" + amino_freq.N.toFixed(1) + "%)" + "
Asp (D)" + "" + amino_content.D + " (" + amino_freq.D.toFixed(1) + "%)" + "
" + "		" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Cys (C)" + "" + amino_content.C + " (" + amino_freq.C.toFixed(1) + "%)" + "
Gln (Q)" + "" + amino_content.Q + " (" + amino_freq.Q.toFixed(1) + "%)" + "
Glu (E)" + "" + amino_content.E + " (" + amino_freq.E.toFixed(1) + "%)" + "
Gly (G)" + "" + amino_content.G + " (" + amino_freq.G.toFixed(1) + "%)" + "
" + "		" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
His (H)" + "" + amino_content.H + " (" + amino_freq.H.toFixed(1) + "%)" + "
Ile (I)" + "" + amino_content.I + " (" + amino_freq.I.toFixed(1) + "%)" + "
Leu (L)" + "" + amino_content.L + " (" + amino_freq.L.toFixed(1) + "%)" + "
Lys (K)" + "" + amino_content.K + " (" + amino_freq.K.toFixed(1) + "%)" + "
" + "		" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Met (M)" + "" + amino_content.M + " (" + amino_freq.M.toFixed(1) + "%)" + "
Phe (F)" + "" + amino_content.F + " (" + amino_freq.F.toFixed(1) + "%)" + "
Pro (P)" + "" + amino_content.P + " (" + amino_freq.P.toFixed(1) + "%)" + "
Ser (S)" + "" + amino_content.S + " (" + amino_freq.S.toFixed(1) + "%)" + "
" + "		" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Thr (T)" + "" + amino_content.T + " (" + amino_freq.T.toFixed(1) + "%)" + "
Trp (W)" + "" + amino_content.W + " (" + amino_freq.W.toFixed(1) + "%)" + "
Tyr (Y)" + "" + amino_content.Y + " (" + amino_freq.Y.toFixed(1) + "%)" + "
Val (V)" + "" + amino_content.V + " (" + amino_freq.V.toFixed(1) + "%)" + "
" + "
" + "
" + "Amino acid counting" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Total number:" + "" + total_aminos + "
Positively charged (Arg+Lys):" + "" + (amino_content.R + amino_content.K) + " (" + ((amino_content.R + amino_content.K)*100/total_aminos).toFixed(1) + "%)" + "
Negatively charged (Asp+Glu):" + "" + (amino_content.D + amino_content.E) + " (" + ((amino_content.D + amino_content.E)*100/total_aminos).toFixed(1) + "%)" + "
Aromatic (Phe+His+Try+Tyr):" + "" + (amino_content.F + amino_content.H + amino_content.W + amino_content.Y) + " (" + ((amino_content.F + amino_content.H + amino_content.W + amino_content.Y)*100/total_aminos).toFixed(1) + "%)" + "
" + "		" + "Biochemical parameters" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Atomic composition:" + "" + atomic_composition_output + "
Molecular mass [Da]:" + "" + molecular_weight.toFixed(1) + "
Theoretical pI:" + "" + pI.toFixed(2) + "
Extinction coefficient at 280 nm [M-1 cm-1]:" + "" + extinction_coeffs[1].toFixed(0) + " / " + extinction_coeffs[0].toFixed(0) + " (all Cys red/ox)" + "
" + "
Plot for hydrophobicity, charge, predicted secondary structure and predicted solvent accessability"

+ HydrophobicityChargePlot

+ "
Codon usage" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (<a href=\"http://en.wikipedia.org/wiki/Codon_Adaptation_Index\">CAI</a>):" + codon_usage[0] + "" + codon_usage[3] + "" + codon_usage[1] + "" + codon_usage[4] + "" + codon_usage[5] + "" + codon_usage[2] + "
" + "
Predictions (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)" + "
The BioBrick-AutoAnnotator was created by <a href=\"https://2013.igem.org/Team:TU-Munich\">TU-Munich 2013</a> iGEM team. For more information please see the <a href=\"https://2013.igem.org/Team:TU-Munich/Results/Software\">documentation</a>.
If you have any questions, comments or suggestions, please leave us a <a href=\"https://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator\">comment</a>." + "
"

+ "
";

$("#htmlTable").html(htmlCode); $("#htmlExplanation").html("The generated table giving various computed parameters: (The wiki-code producing this table is below)");

$("#wikiTable").text("" + htmlCode + HydrophobicityChargePlotScript + ""); $("#wikiTable").css("display","block"); $("#wikiExplanation").html("Copy the following into the wiki to get the protein-data-table:");

$("#wikiTable").focus(); $("#wikiTable").select(); } catch(err){ txt="There was an error while compiling the output.\n\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } alert(txt); return; //to end execution }

};


function show_or_hide_plot(){ try { if( $('#hydrophobicity_charge_button').val() =='Show' ){ $('#hydrophobicity_charge_container').css('display','block'); //draw the plots for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){ $.plot('#hydrophobicity_charge_placeholder'+ plot_num.toString(), [{ color: 'rgba(100,149,237,1)', data: hydrophobicity_datapoints, label: 'Hydrophobicity', lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' }, yaxis: 1 }, { color: 'rgba(255,99,71,1)', data: charge_datapoints, label: 'Charge', lines: { show: true, fill: true, fillColor: 'rgba(255,99,71,0.1)' }, yaxis: 2 }], flot_plot_options[plot_num] ); } $('#hydrophobicity_charge_button').val('Hide'); $('#hydrophobicity_charge_explanation').html('
Moving average over 5 amino acids for hydrophobicity (blue) and charge (red)'); } else{ //so is on hide $('#hydrophobicity_charge_container').css('display','none'); $('#hydrophobicity_charge_button').val('Show'); $('#hydrophobicity_charge_explanation').html(); } } catch(err){ txt="There was an error with the button controlling the visibility of the plot.\n"; txt=txt+"The originating error is:\n" + err + "\n\n"; alert(txt); } };

function readout_result_sorter(a,b){ //sorts the elements of the lists for the gene ontology output and the alignment output into the required order return (b[1] - a[1]); };

function find_sequence_features(local_coding_nuc_sequence,local_amino_sequence){ //returns the object Features with EXTERNAL index as property and feature as value try{ var Features = {};

//first look for RFC25 scars for ( i = 0 ; i < local_coding_nuc_sequence.length ; i = i + 3){ var codonpair = local_coding_nuc_sequence.substr(i,6); if (codonpair == "ACCGGC"){ Features[(i/3) + 1] = "TG"; } } //find forbidden restriction sites?

//var motives_found = amino_sequence.match(search_regexp);

while ((match = search_regexp.exec(local_amino_sequence)) != null) { Features[match.index + 1] = match[0]; // match.index gives the location of the first aa in the feature BUT starting from 0 search_regexp.lastIndex = match.index + 1; // to look for overlapping features }

return Features; } catch(err){ txt = "An error occured while finding sequence features and preparing the output.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };


function clean_sequence(sequence_to_clean){ try{ var cleanedSequence = sequence_to_clean.replace(/ /g, ""); // remove spaces var cleanedSequence2= cleanedSequence.toUpperCase(); // convert to upper case var cleanedSequence3= cleanedSequence2.replace(/\r?\n|\r/g, ""); // remove line breaks var wrongLetter = cleanedSequence3.search(/[^ATGC]/); // check for wrong nucleotides if (wrongLetter > -1){ throw "Unknown nucleotide in the entered sequence. Only use A, T, G, C!"; } return cleanedSequence3; } catch(err){ txt = "An error occured while checking and cleaning up the provided sequence.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };

function count_amino_acids(aa_sequence){ try{ //Counts standard amino acids, returns an array {AminoAcid:Number} var local_amino_acids_content = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,I:0,L:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0}; var local_amino_acids_freq = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,I:0,L:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0}; for (i=0; i<aa_sequence.length; i++){ local_amino_acids_content[aa_sequence[i]]++; } var aa_total=aa_sequence.length; for (aa in amino_acids){ local_amino_acids_freq[aa] = local_amino_acids_content[aa] * (100 / aa_total); }; return [local_amino_acids_content,local_amino_acids_freq]; } catch(err){ txt = "An error occured while counting the amino acids.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };

function compute_molecular_weight_and_atomic_composition(amino_acids_content){ try{ var molec_weight = water_weight; var atomic_comp = [0,2,0,1,0]; //a water molecule for (aa in amino_acids){ molec_weight = molec_weight + amino_acids_content[aa] * amino_weights[aa]; for ( i=0 ; i < 5 ; i++ ){ atomic_comp[i] = atomic_comp[i] + amino_acids_content[aa] * atomic_composition_of_aa[aa][i]; } } return [molec_weight,atomic_comp]; } catch(err){ txt = "An error occured while computing the molecular weight of the protein.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };

function compute_pI(local_aa_sequence,pI_amino_acids_content){ try{ var nterm = local_aa_sequence[0]; //the first aa var composition = {Nterm:1,Cterm:1, K:pI_amino_acids_content.K, R:pI_amino_acids_content.R, H:pI_amino_acids_content.H, D:pI_amino_acids_content.D, E:pI_amino_acids_content.E, C:pI_amino_acids_content.C, Y:pI_amino_acids_content.Y}; var pos_pKs = jQuery.extend(true, {}, positive_pKs); //to clone positive_pKs, otherwise just passes reference if ( nterm in pKnterminal ){ pos_pKs.Nterm = pKnterminal[nterm]; }

var pHOld = 0.0; //just to set off the while loop var pHNew = 7.0; var step = 3.5; var charge = charge_at_pH(pHNew,composition,pos_pKs); while ( Math.abs(pHOld - pHNew) > 0.0001 && Math.abs(charge)!=0 ){ pHOld = pHNew; //store the now old pH if (charge >0){ pHNew = pHNew + step; } else { //so charge < 0 pHNew = pHNew - step; } step = step/2; charge = charge_at_pH(pHNew,composition,pos_pKs); } var pH = pHNew; return pH; } catch(err){ txt = "An error occured while computing the theoretical pI.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };

function charge_at_pH(pH, compo, local_pos_pKs){ try{ var charge = 0; for (aa in positive_pKs){ charge = charge + compo[aa] * (1/(1+Math.pow(10, pH - local_pos_pKs[aa]))); } for (aa in negative_pKs){ charge = charge - compo[aa] * (1/(1+Math.pow(10, negative_pKs[aa] - pH))); } return charge; } catch(err){ txt = "An error occured while computing the charge of the protein at a certain pH.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };

function compute_extinction_coeff(local_amino_acid_content){ try{ var E_allCystine = local_amino_acid_content.Y * extinction.Y + local_amino_acid_content.W * extinction.W + (local_amino_acid_content.C /2)*extinction.Cystine; var E_noCystine = local_amino_acid_content.Y * extinction.Y + local_amino_acid_content.W * extinction.W ; return [E_allCystine,E_noCystine]; } catch(err){ txt = "An error occured while computing the extinction coefficient of the protein.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };

function find_reading_frame(nuc_sequence){ try{ // atg_position is the first nucleotide in the ATG (start codon) // stop_position is the first nucleotide in the stop codon isRFC25=false; //GLOBAL VARIABLE // check for RFC 25 var ideal_stop = nuc_sequence.length - 3; if (nuc_sequence.length%3 == 0 && !(nuc_sequence.substr(ideal_stop,3) in stop_codons)){ isRFC25 = confirm("Is this part in RFC25, i.e. the start codon is part of the prefix?\n If it is RFC25, press 'OK', otherwise 'Cancel'"); }

if ( !isRFC25 ){ //so not RFC25

var atg_position = nuc_sequence.indexOf("ATG"); if ( atg_position > -1){ var stop_position = -1; for ( i = atg_position + 3 ; i < nuc_sequence.length ; i = i + 3){ var codon = nuc_sequence.substr(i,3); if ( codon in stop_codons ){ stop_position = i; break; } } if (stop_position == -1){ if ((nuc_sequence.length - atg_position)%3 == 0){

stop_position = nuc_sequence.length + 3; //so RFC10 using stop codon in suffix alert("Using stop codon in suffix of RFC10"); } else { alert("No stop codon found in frame & can't use stop codon in suffix of RFC10"); return; } } } else { alert("No ATG found, something is wrong! Might be RFC25?"); return; } var reading_length = stop_position - atg_position + 3; if ( (reading_length / nuc_sequence.length) < 0.6){ real_atg_position = prompt("The reading length is small compared to the length of the sequence, please enter the position of the start codon (start of sequence is 1)",atg_position + 1); atg_position = real_atg_position - 1; stop_position= -1; for ( i = atg_position + 3 ; i < nuc_sequence.length ; i = i + 3){ if (nuc_sequence.substr(i,3) in stop_codons ){ stop_position = i; break; } } if (stop_position == -1 && atg_position > -1){ if ((nuc_sequence.length - atg_position)%3 == 0){ stop_position = nuc_sequence.length + 3; //so RFC10 using stop codon in suffix alert("Using stop codon in suffix of RFC10"); } else { alert("No stop codon found in frame & can't use stop codon in suffix of RFC10"); return; } } } } else { // so RFC25 atg_position = -9; stop_position = nuc_sequence.length + 6; }

var reading_frame_start_found = atg_position; var reading_frame_end_found = stop_position - 1; //the last nucleotide to be translated

return [reading_frame_start_found,reading_frame_end_found]; } catch(err){ txt = "An error occured while determining the appropriate open reading frame (ORF) of the provided sequence.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } };

function translate_to_aa_and_codon_count(nuc_sequence){ try{ var local_amino_sequence = ""; var local_codon_count = { 'TTT': 0, 'TTC': 0, 'TTA': 0, 'TTG': 0, 'TCT': 0, 'TCC': 0, 'TCA': 0, 'TCG': 0, 'TAT': 0, 'TAC': 0, 'TGT': 0, 'TGC': 0, 'TGG': 0, 'CTT': 0, 'CTC': 0, 'CTA': 0, 'CTG': 0, 'CCT': 0, 'CCC': 0, 'CCA': 0, 'CCG': 0, 'CAT': 0, 'CAC': 0, 'CAA': 0, 'CAG': 0, 'CGT': 0, 'CGC': 0, 'CGA': 0, 'CGG': 0, 'ATT': 0, 'ATC': 0, 'ATA': 0, 'ATG': 0, 'ACT': 0, 'ACC': 0, 'ACA': 0, 'ACG': 0, 'AAT': 0, 'AAC': 0, 'AAA': 0, 'AAG': 0, 'AGT': 0, 'AGC': 0, 'AGA': 0, 'AGG': 0, 'GTT': 0, 'GTC': 0, 'GTA': 0, 'GTG': 0, 'GCT': 0, 'GCC': 0, 'GCA': 0, 'GCG': 0, 'GAT': 0, 'GAC': 0, 'GAA': 0, 'GAG': 0, 'GGT': 0, 'GGC': 0, 'GGA': 0, 'GGG': 0, 'TAA': 0, //STOP CODONS, shouldn't appear and already be removed 'TAG': 0, 'TGA': 0 }; for ( i = 0 ; i < nuc_sequence.length ; i = i + 3){ var codon = nuc_sequence.substr(i,3); local_codon_count[codon] ++; //count the number of each codon appearing local_amino_sequence = local_amino_sequence + translation_table[codon]; } return [local_amino_sequence,local_codon_count]; } catch(err){ txt = "An error occured while translating the nucleotide sequence into the amino acid sequence.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; }

};

function analyze_codons(local_codon_count,local_amino_content){ try{ var total_synon_codons = 0; var E_coli_prod = 1; var Yeast_prod = 1; var Mammalian_prod = 1; var Arabidopsis_prod = 1; var Subtilis_prod = 1; var Physco_prod = 1;

for (codon in local_codon_count){ if (codon in non_synonymous_codons){ //ignore the non-synonymous codons continue; }

total_synon_codons = total_synon_codons + local_codon_count[codon]; //should give the total number of codons (excluding stop codons) E_coli_prod = E_coli_prod * Math.pow( E_coli_codon_weights[codon], local_codon_count[codon]); Yeast_prod = Yeast_prod * Math.pow( Yeast_codon_weights[codon], local_codon_count[codon]); Mammalian_prod = Mammalian_prod * Math.pow( Mouse_codon_weights[codon], local_codon_count[codon]); Subtilis_prod = Subtilis_prod * Math.pow( Subtilis_codon_weights[codon], local_codon_count[codon]); Arabidopsis_prod = Arabidopsis_prod * Math.pow(Arabidopsis_codon_weights[codon], local_codon_count[codon]); Physco_prod = Physco_prod * Math.pow( Physco_codon_weights[codon], local_codon_count[codon]); };

var E_coli_CAI = Math.pow( E_coli_prod, 1/total_synon_codons); var Yeast_CAI = Math.pow( Yeast_prod, 1/total_synon_codons); var Mammalian_CAI = Math.pow( Mammalian_prod, 1/total_synon_codons); var Subtilis_CAI = Math.pow( Subtilis_prod, 1/total_synon_codons); var Arabidopsis_CAI = Math.pow( Arabidopsis_prod, 1/total_synon_codons); var Physco_CAI = Math.pow( Physco_prod, 1/total_synon_codons);

var usageOutput = [ E_coli_CAI , Yeast_CAI , Mammalian_CAI , Subtilis_CAI , Arabidopsis_CAI , Physco_CAI]; return usageOutput; } catch(err){ txt = "An error occured while analyzing the codon usage of the provided sequence.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; } }

function compute_hydrophobicity_charge_plot(foobar_amino_sequence){ try{ var window_size = 5; //take average over 5 amino acids if (window_size < foobar_amino_sequence.length + 1){ var hydrophobicity_charge_output = [[],[]]; //an array of two arrays, first array for hydrophobicity, second for charge var hydrophobicity_0 = 0; var charge_0 = 0; for ( i = 0 ; i < window_size ; i++ ){ //compute the first window hydrophobicity_0 = hydrophobicity_0 + k_d_hydrophobicity[foobar_amino_sequence[i]]/window_size; charge_0 = charge_0 + emboss_charge[foobar_amino_sequence[i]]/window_size; } hydrophobicity_charge_output[0][0] = hydrophobicity_0; hydrophobicity_charge_output[1][0] = charge_0; for ( window_start = 1 ; window_start < (foobar_amino_sequence.length - window_size + 1) ; window_start ++){ hydrophobicity_charge_output[0][window_start] = hydrophobicity_charge_output[0][window_start - 1] - k_d_hydrophobicity[foobar_amino_sequence[window_start - 1]]/window_size + k_d_hydrophobicity[foobar_amino_sequence[window_start + 4]]/window_size; hydrophobicity_charge_output[1][window_start] = hydrophobicity_charge_output[1][window_start - 1] - emboss_charge[foobar_amino_sequence[window_start - 1]]/window_size + emboss_charge[foobar_amino_sequence[window_start + 4]]/window_size; } } else{ //so sequence is to short for a plot hydrophobicity_charge_output = "sequence too short"; } return hydrophobicity_charge_output; } catch(err){ txt = "An error occured while computing the hydrophobicity and charge of the subsequences.\n"; if ((err.toString()).substr(0,16) == "An error occured"){ txt = txt + "This error originated at a lower level: \n\n" + err.toString(); } else{ txt=txt + "The originating error is: \n" + err + "\n\n"; } throw txt; }

}
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