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Last active August 29, 2015 14:25
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DNA/RNA Transcript Tool
Raw
index.html
<head>
<title>DNA Transcript Tool</title>
</head>
<div class="container-fluid">
<nav class="navbar navbar-default">
<div class="container-fluid">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">DNA Transcript Tool</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
</div>
</div>
</nav>
<div class="row">
<div class="col-md-6 col-md-offset-3 input-area">
<h4>Input Sequence Here</h4>
<textarea class="form-control" id="sequence-input" rows="3"></textarea>
<div class="radio">
<label>
<input type="radio" name="optionsRadios" id="optionsRadios1" value="option1" checked> DNA → RNA
</label>
</div>
<div class="radio">
<label>
<input type="radio" name="optionsRadios" id="optionsRadios2" value="option2"> RNA → DNA
</label>
</div>
<div class="radio">
<label>
<input type="radio" name="optionsRadios" id="optionsRadios3" value="option3"> Find Possible Coding Sequences (RNA Input)
</label>
</div>
<div class="radio">
<label>
<input type="radio" name="optionsRadios" id="optionsRadios4" value="option4"> Find Possible Coding Sequences (DNA Input)
</label>
</div>
<button type="submit" class="btn btn-primary" id="submit-button">Submit</button>
</div>
</div>
<div class="row">
<div class='col-md-10 col-md-offset-1 results-area'>
<h1>Results</h1>
<div id="results-text">
<div id="instructions" class="col-md-6 col-md-offset-3">
<h3>Welcome</h3>
<p>This simple tool is designed to do two things: Translate DNA into RNA (and vice versa) and find all possible coding sequences in a given sequence of DNA. Start codons are AUG and stop codons are UAG, UAA, and UGA </p>
<p><ol>Instructions:
<li>Enter your DNA or RNA sequence above</li>
<li>Select the appropriate options</li>
<li>Click submit to see the results here.</li></ol></p>
</div>
</div>
</div>
</div>
</div>
Raw
script.js
function StartCodons(rna_sequence) {
var re = /(AUG)/g,
str = rna_sequence;
var start_indexes = [];
while ((match = re.exec(str)) != null) {
start_indexes.push(match.index);
}
return start_indexes;
}
function FindStop(start_codon, rna_sequence) {
index = start_codon;
for (i = 0; i < rna_sequence.slice(start_codon, rna_sequence.length).length / 3; i++) {
current_codon = rna_sequence.slice(index, index + 3)
index += 3
if (current_codon == "UAA" | current_codon == "UAG" | current_codon == "UGA") {
return index;
};
}
return "N/A"
}
function sequences(rna_sequence) {
starts = StartCodons(rna_sequence);
stops = [];
for (var i = 0; i < starts.length; i++) {
stops.push(FindStop(starts[i], rna_sequence))
}
sequence_array = []
start_stop_pair = []
for (var i = 0; i < starts.length; i++) {
seq_str = rna_sequence.slice(starts[i], stops[i])
if (seq_str !== "" & seq_str.length > 6) {
sequence_array.push(seq_str);
start_stop_pair.push(starts[i] + ":" + stops[i])
}
}
return [sequence_array, start_stop_pair];
}
bases = ['u', 'c', 'a', 'g']
codons = []
amino_acids = 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG'
for (i = 0; i < bases.length; i++) {
for (j = 0; j < bases.length; j++) {
for (p = 0; p < bases.length; p++) {
codons.push(bases[i] + bases[j] + bases[p])
}
}
}
function AATranslate(sequence) {
codon_list = sequence.match(/(...)/g);
AAseq = ''
for (var i = 0; i < codon_list.length; i++) {
AAseq = AAseq.concat(amino_acids[codons.indexOf(codon_list[i].toLowerCase())])
}
return AAseq;
}
function dna_rna(sequence) {
sequence = sequence.toUpperCase();
rna = ''
for (var i = 0; i < sequence.length; i++) {
if (sequence[i] == 'T') {
rna += 'U'
} else {
rna += sequence[i]
}
}
return rna;
}
function rna_dna(sequence) {
sequence = sequence.toUpperCase();
rna = ''
for (var i = 0; i < sequence.length; i++) {
if (sequence[i] == 'U') {
rna += 'T'
} else {
rna += sequence[i]
}
}
return rna;
}
$(document).ready(function() {
$("#submit-button").click(function() {
var sequence = $("#sequence-input").val();
if ($("#optionsRadios1").is(":checked")) {
$("#results-text").replaceWith("<div id='results-text'><div class='single-result'><h4>RNA Sequence: </h4><p>" + dna_rna(sequence) + "</p></div></div>")
} else if ($("#optionsRadios2").is(":checked")) {
$("#results-text").replaceWith("<div id='results-text'>" + rna_dna(sequence) + "</div>")
} else if ($("#optionsRadios3").is(":checked")) {
var gene_matches = sequences(sequence)[0];
var nucleotide_indexes = sequences(sequence)[1];
$("#results-text").replaceWith("<div id='results-text'></div>")
for (var j = 0; j < gene_matches.length; j++) {
$("#results-text").append("<div class='single-result'><hr><p>RNA Transcript - " + nucleotide_indexes[j] + gene_matches[j] + "</p><p>Amino Acid Sequence - " + AATranslate(gene_matches[j]) + "<p></div>")
}
} else if ($("#optionsRadios4").is(":checked")) {
var gene_matches = sequences(dna_rna(sequence))[0];
var nucleotide_indexes = sequences(dna_rna(sequence))[1];
$("#results-text").replaceWith("<div id='results-text'></div>")
for (var j = 0; j < gene_matches.length; j++) {
$("#results-text").append("<div class='single-result'><hr><p><h4>RNA Transcript - " + nucleotide_indexes[j] + "</h4>" + gene_matches[j] + "</p><p><h4>Amino Acid Sequence</h4> " + AATranslate(gene_matches[j]) + "<p></div>")
}
}
})
})
Raw
scripts
<script src="//cdnjs.cloudflare.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js"></script>
Raw
style.css
hr {
background-color: black;
height: 1px;
}
.input-area {
background-color: lightgrey;
border: 1px solid grey;
margin-bottom: 50px;
border-radius: 10px;
}
#sequence-input {
margin-bottom: 10px;
}
.btn-primary {
margin-bottom: 10px;
}
.results-area {
background-color: lightgrey;
border-radius: 10px;
word-wrap: break-word;
border: 1px grey solid;
}
.results-area h1{
text-align: center;
}
#instructions {
font-size: 120%;
}
#instructions h3 {
text-align: center;
font-size: 175%;
}
.single-result {
margin: 0 40px;
}
Raw
styles
<link href="//maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" rel="stylesheet" />
Raw
Tool.markdown
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