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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Salt: Sequence alignment tool | GEAR</title>
<meta name="description" content="Sequence alignment tool.">
<link rel="stylesheet" href="https://www.gear-genomics.com/libs/bootstrap/4.0.0/css/bootstrap.min.css" crossorigin="anonymous">
<link rel="stylesheet" href="https://www.gear-genomics.com/libs/fontawesome-free-6.2.1-web/css/all.min.css">
<link rel="stylesheet" href="static/css/gear.css">
</head>
<body>
<header class="px-0 py-4">
<div class="container">
<h1 class="display-4 app-name">Salt</h1>
<p class="lead">Sequence alignment tool. Heavily based on <a target="_blank" href="bioseq.html">bioseq</a></p>
<a class="plain" href="https://www.gear-genomics.com/contact" target="_blank">
<i class="fas fa-question"></i> Get help
</a>
·
<a class="plain" href="https://www.gear-genomics.com/citation" target="_blank">
<i class="fas fa-user-graduate"></i> Citation
</a>
·
<a class="plain" target="_blank" href="https://github.com/gear-genomics/salt">
<i class="fab fa-github-alt"></i> Source
</a>
</div>
</header>
<main class="container">
<ul class="nav nav-fill mb-4" id="mainTab">
<li class="nav-item">
<a class="nav-link active" href="#input-tab">Input</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#result-tab" id="link-results">Results</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#help-tab" id="link-help">Help</a>
</li>
</ul>
<div class="tab-content" id="main-tabs">
<div class="tab-pane show active" id="input-tab">
<div class="card">
<div class="card-body">
<h5 class="card-title">Reference Sequence</h5>
<div class="form-group">
<label for="inputFileRef">
Paste sequence below or upload file (<code>.gb</code> or <code>.txt</code>)
</label>
<input type="file" class="form-control-file" id="inputFileRef">
</div>
<div class="form-group">
<textarea class="form-control" id="target" rows="6"></textarea>
</div>
</div>
</div>
<br />
<div class="card">
<div class="card-body">
<h5 class="card-title">Query Sequence</h5>
<div class="row">
<div class="col-sm-6">
<div class="form-group">
<label for="inputFileQuery">
Paste sequence below or upload file (<code>.gb</code> or <code>.txt</code>)
</label>
<input type="file" class="form-control-file" id="inputFileQuery">
</div>
</div>
<div class="col-sm-6">
<div class="form-group">
<br/>
<button type="button" class="btn btn-secondary btn-sm float-right" id="reverseQueryBtn">
Reverse-Complement Query</button>
</div>
</div>
</div>
<div class="form-group">
<textarea class="form-control" id="query" rows="6"></textarea>
</div>
</div>
</div>
<br />
<div class="card">
<div class="card-body">
<h5 class="card-title">Settings</h5>
<div class="row">
<div class="col-sm-2 align-self-center">
<div class="form-group">
Local Alignment: <input type="checkbox" id="is_local" checked/>
</div>
</div>
<div class="col-sm-2 align-self-center">
<div class="form-group">
Match Score: <input size="2" value="1" id="match"/>
</div>
</div>
<div class="col-sm-2 align-self-center">
<div class="form-group">
Mismatch: <input size="2" value="-2" id="mismatch"/>
</div>
</div>
<div class="col-sm-2 align-self-center">
<div class="form-group">
Gap Open: <input size="2" value="-2" id="gapo"/>
</div>
</div>
<div class="col-sm-2 align-self-center">
<div class="form-group">
Extension: <input size="2" value="-1" id="gape"/>
</div>
</div>
<div class="col-sm-2 align-self-center">
<div class="form-group">
Start Count: <input size="2" value="1" id="startCount"/>
</div>
</div>
</div>
</div>
</div>
<br />
<button type="submit" class="btn btn-outline-primary" id="btn-submit">
<i class="fas fa-rocket" style="margin-right: 5px;"></i>
Launch Analysis
</button>
<button type="submit" class="btn btn-outline-primary" id="btn-example">
<i class="fas fa-eye" style="margin-right: 5px;"></i>
Load Example
</button>
</div>
<div class="tab-pane" id="result-tab">
<div class="form-group">
<button type="submit" class="btn btn-outline-primary" id="btn-save">
<i class="far fa-save" style="margin-right: 5px;"></i>
Save Complete Results (.txt)
</button>
<button type="submit" class="btn btn-outline-primary" id="btn-save-fa">
<i class="far fa-save" style="margin-right: 5px;"></i>
Save Padded Alignment (.fa)
</button>
</div>
<pre id="out"></pre>
<br />
<span id="runtime" style="color: gray;"></span>
</div>
<div class="tab-pane" id="help-tab">
<h4>Application Description</h4>
<p> Salt is a tool to align a reference (target sequence) to a query sequence.
Just supply two files and hit submit.</p>
<h4>Accepted Input</h4>
<p> The sequence files can be provided in gb or txt format (*.gb and *.txt).</p>
<h4>Sample Data</h4>
<p> The "Show Example" button loads an sample trace file.
</p>
</div>
</div>
</main>
<footer>
<div class="container">
<div class="float-left">
<a class="plain" target="_blank" href="https://gear.embl.de">
GEAR ~
<i class="fas fa-home"></i>
</a>
·
<a class="plain" target="_blank" href="https://github.com/gear-genomics">
<i class="fab fa-github-alt"></i>
</a>
·
<a class="plain" target="_blank" href="https://gear.embl.de/terms">
Terms of Use
</a>
·
<a class="plain" target="_blank" href="https://gear.embl.de/contact">
Contact Us
</a>
</div>
<div class="float-right">
Hosted with
<i class="fas fa-heart embl-red"></i> by
<a class="plain" target="_blank" href="https://www.embl.de/">
<img class="footer-logo" alt="EMBL logo" src="static/img/embl.svg">
</a>
</div>
</div>
</footer>
<script src="https://www.gear-genomics.com/libs/js/jquery-3.2.1.slim.min.js" crossorigin="anonymous"></script>
<script src="https://www.gear-genomics.com/libs/js/popper-1.12.9/popper.min.js" crossorigin="anonymous"></script>
<script src="https://www.gear-genomics.com/libs/bootstrap/4.0.0/js/bootstrap.min.js" crossorigin="anonymous"></script>
<script src="static/js/bioseq.js"></script>
<script src="static/js/salt.js"></script>
</body>
</html>