Team:TU-Munich/AnnotatorCode.js

From 2013.igem.org

(Difference between revisions)

Revision as of 11:53, 28 July 2013

/**

*  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 };

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

/*from: * Varshavsky (1997). The N-end rule pathway of protein degradation.

		* Varshavsky et al. (1989). Universality and structure of the N-end rule.
*/

var halflife_table_Mammalian = {A: "4.4", R: "1", N: "1.4", D: "1.1", C: "1.2", Q: "0.8", E: "1", G: "30", H: "3.5", I: "20", L: "5.5", K: "1.3", M: "30", F: "1.1", P: ">20", S: "1.9", T: "7.2", W: "2.8", Y: "2.8", V: "100"};

var halflife_table_Yeast = {A: ">20", R: "0.03", N: "0.05", D: "0.05", C: ">20", Q: "0.17", E: "0.5", G: ">20", H: "0.17", I: "0.5", L: "0.05", K: "0.05", M: ">20", F: "0.05", P: ">20", S: ">20", T: ">20", W: "0.05", Y: "0.17", V: ">20"};

var halflife_table_E_coli = {A: ">10", R: "0.03", N: ">10", D: ">10", C: ">10", Q: ">10", E: ">10", G: ">10", H: ">10", I: ">10", L: "0.03", K: "0.03", M: ">10", F: "0.03", P: "unknown", S: ">10", T: ">10", W: "0.03", Y: "0.03", V: ">10"};

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 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 };

// 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 };

/**

*  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){ throw "Not a valid BioBrick name nor a nucleotide sequence. The BioBrick name must contain one letter followed by digits"; } if (numeric_start == -1){ //so entered a sequence //interpret the entered bb number as sequence bb_number = ""; main_table_calc(entered_bb_number,bb_number); } else{ //entered a BioBrick number, so try to get the sequence from the Registry var bb_number = entered_bb_number.substr(numeric_start - 1); 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 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 (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(sequence,bb_number);

} }); } 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,bb_number) { try{ var entered_nuc_sequence = clean_sequence(sequence); var reading_frame = find_reading_frame(entered_nuc_sequence); var reading_frame_start = reading_frame[0]; //the A in the ATG start codon var reading_frame_end = reading_frame[1]; //last nucleotide to be translated //recall internal indexing starts at 0, external indexing at 1

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

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

var amino_output = " "; for ( i=0 ; i < amino_sequence.length /100 ; i++){ amino_output = amino_output + (100*(i) + 1) + " " + amino_sequence.substr(i*100, 100) + "
"; } amino_output = amino_output + "";

var counting_result = count_amino_acids(amino_sequence); var amino_content = counting_result[0]; var amino_freq = counting_result[1]; var total_aminos = amino_sequence.length; var molecular_weight = compute_molecular_weight(amino_content); var pI = compute_pI(amino_sequence,amino_content); var extinction_coeffs = compute_extinction_coeff(amino_content,molecular_weight); var nterm = amino_sequence[0];

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

// Code to display the table htmlCode = htmlCode

+ "" + "" + "" + "" + "" + "" + "" + "" + "" // EXClUDING STOP CODON + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "" + "

BioBrick: <a href=\"http://parts.igem.org/wiki/index.php?title=Part:BBa_" + bb_number + "\">BBa_" + bb_number + "</a>" + "

Automatically determined parameters using the <a href=\"https://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator\">BioBrick-AutoAnnotator</a> version 1.0" + "

RFC standard:" + "

" + RFC_standard + "

ORF from " + (reading_frame_start + 1) + " to " + (reading_frame_end + 1) + " (excluding stop-codon)" + "

Nucleotide sequence: (underlined part encodes the protein, italic parts were added)
" + nuc_sequence_to_display_html + "

Amino acid sequence:
" + amino_output + "

Amino acid composition:

A (Ala)" + "

" + amino_content.A + " (" + amino_freq.A.toFixed(1) + "%)" + "

" + "

C (Cys)" + "

" + amino_content.C + " (" + amino_freq.C.toFixed(1) + "%)" + "

" + "

H (His)" + "

" + amino_content.H + " (" + amino_freq.H.toFixed(1) + "%)" + "

" + "

M (Met)" + "

" + amino_content.M + " (" + amino_freq.M.toFixed(1) + "%)" + "

" + "

T (Thr)" + "

" + amino_content.T + " (" + amino_freq.T.toFixed(1) + "%)" + "

R (Arg)" + "

" + amino_content.R + " (" + amino_freq.R.toFixed(1) + "%)" + "

" + "

Q (Gln)" + "

" + amino_content.Q + " (" + amino_freq.Q.toFixed(1) + "%)" + "

" + "

I (Ile)" + "

" + amino_content.I + " (" + amino_freq.I.toFixed(1) + "%)" + "

" + "

F (Phe)" + "

" + amino_content.F + " (" + amino_freq.F.toFixed(1) + "%)" + "

" + "

W (Trp)" + "

" + amino_content.W + " (" + amino_freq.W.toFixed(1) + "%)" + "

N (Asn)" + "

" + amino_content.N + " (" + amino_freq.N.toFixed(1) + "%)" + "

" + "

E (Glu)" + "

" + amino_content.E + " (" + amino_freq.E.toFixed(1) + "%)" + "

" + "

L (Leu)" + "

" + amino_content.L + " (" + amino_freq.L.toFixed(1) + "%)" + "

" + "

P (Pro)" + "

" + amino_content.P + " (" + amino_freq.P.toFixed(1) + "%)" + "

" + "

Y (Tyr)" + "

" + amino_content.Y + " (" + amino_freq.Y.toFixed(1) + "%)" + "

D (Asp)" + "

" + amino_content.D + " (" + amino_freq.D.toFixed(1) + "%)" + "

" + "

G (Gly)" + "

" + amino_content.G + " (" + amino_freq.G.toFixed(1) + "%)" + "

" + "

K (Lys)" + "

" + amino_content.K + " (" + amino_freq.K.toFixed(1) + "%)" + "

" + "

S (Ser)" + "

" + amino_content.S + " (" + amino_freq.S.toFixed(1) + "%)" + "

" + "

V (Val)" + "

" + 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) + "%)" + "

Biochemical parameters:" + "

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)" + "

Estimated half-life [h]:" + "

E. coli:" + "

" + halflife_table_E_coli[nterm] + "

S. cervisiae:" + "

" + halflife_table_Yeast[nterm] + "

Mammals:" + "

" + halflife_table_Mammalian[nterm] + "

Codon usage (CAI):" + "

E. coli:" + "

" + codon_usage[0] + "

S. cervisiae:" + "

" + codon_usage[1] + "

Mammals:" + "

" + codon_usage[2] + "

The AutoAnnotator was created by <a href=\"https://2013.igem.org/Team:TU-Munich\">TU-Munich 2013</a> iGEM team, for more information see the <a href=\"https://2013.igem.org/Team:TU-Munich/Results/Software\">description</a>. If you have any comments or suggestions, please <a href=\"mailto:igem@wzw.tum.de?Subject=AutoAnnotator\" target=\"_top\">email us</a>." + "

"

+ "
";

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

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

} catch(err){ txt="There was an error on this page.\n\n"; if ((err.toString()).substr(0,17) == "The 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 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 var isRFC25=false; // 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 { throw "No stop codon found in frame & can't use stop codon in suffix of RFC10"; } } } else { throw "No ATG found, something is wrong! Might be RFC25?"; } 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) == ("TAA"|"TAG"|"TGA") ){ 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 { throw "No stop codon found in frame & can't use stop codon in suffix of RFC10"; } }

} } else { // so RFC25 atg_position = -9; stop_position = nuc_sequence.length + 6; }

var reading_frame_start = atg_position; var reading_frame_end = stop_position - 1; //the last nucleotide to be translated

return [reading_frame_start,reading_frame_end]; } catch(err){ txt = "An error occured while determining the appropriate open reading frame (ORF) of the provided sequence.\n"; if ((err.toString()).substr(0,17) == "The 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(codon_count){ try{ var total_synon_codons = 0; var E_coli_prod = 1; var Yeast_prod = 1; var Mammalian_prod = 1;

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

total_synon_codons = total_synon_codons + 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], codon_count[codon]); Yeast_prod = Yeast_prod * Math.pow( Yeast_codon_weights[codon], codon_count[codon]); Mammalian_prod = Mammalian_prod * Math.pow( Mouse_codon_weights[codon], codon_count[codon]);

//could count weak codons };

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);

@@ Line 460: / Line 460: @@
 		+	"<td colspan=\"100\" width=\"10.0%\">" + codon_usage[2] + "</td>"
 		+	"</tr><tr>"
-		+	"<td colspan=\"1000\" width=\"100.0%\"> 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 read the <a href=\"https://2013.igem.org/Team:TU-Munich/Results/Software\">description</a>. If you have any comments or suggestions, please <a href=\"mailto:igem@wzw.tum.de?Subject=AutoAnnotator\" target=\"_top\">email us</a>." + "</td>"
+		+	"<td colspan=\"1000\" width=\"100.0%\"> The AutoAnnotator was created by <a href=\"https://2013.igem.org/Team:TU-Munich\">TU-Munich 2013</a> iGEM team, for more information see the <a href=\"https://2013.igem.org/Team:TU-Munich/Results/Software\">description</a>. If you have any comments or suggestions, please <a href=\"mailto:igem@wzw.tum.de?Subject=AutoAnnotator\" target=\"_top\">email us</a>." + "</td>"
 		+	"</tr></table>"
 		+	"<br>";