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Gotoh-Local.html
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<!--
University of Freiburg WS 2017/2018
Chair for Bioinformatics
Supervisor: Martin Raden
Authors: Alexander Mattheis, Martin Raden
-->
<div class="gotoh_local_static_size"> <!-- to avoid that MathJax disrupts the output -->
<div id="algorithm_description">
<div class="description">
The algorithms <a href="http://rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Gotoh">Gotoh</a>
and <a href="http://rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Smith-Waterman">Smith-Waterman</a>
combined into one approach.
It computes the local affine alignment of two sequences when using an affine gap scoring.
<br />
<br />
In order to find such a local alignment, the global affince alignment algorithm by
<a href="https://doi.org/10.1016/0022-2836(82)90398-9">Osamu Gotoh (1982)</a>
is extended with an additional case '0' in the recursion function for the matrix $S$.
This lower bound on the similarity score excludes alignments with scores less than zero.
<br />
<br />
For the given input, the according tables $S,P$ and $Q$ are provided along with a list
of according optimal alignments.
On table cell selection, optimal traceback options are shown.
On alignment selection, an according traceback path is visualized in the table.
</div>
<div class="picture">
<img src="Gotoh-Local-120x90.png" />
</div>
</div>
<h1>Input:</h1>
<div id="algorithm_input">
<div class="row">
<div class="colW100"><label>Sequence $a$:</label></div>
<div class="colW400"><input class="sequence" data-bind="value: input.sequence1" id="sequence_1" placeholder="EXAMPLE 'ATC'"
title="Allowed are A-Z and '-'." type="text"></div>
</div>
<div class="row">
<div class="colW100"><label>Sequence $b$:</label></div>
<div class="colW400"><input class="sequence" data-bind="value: input.sequence2" id="sequence_2" placeholder="EXAMPLE 'AGTC'"
title="Allowed are A-Z and '-'." type="text"></div>
</div>
<div class="row">
<div class="colW100"><label>Scoring in $s$:</label></div>
<div class="colW400">
<span class="group"> <!-- Microsoft Browsers will fallback on text-fields using following input type -->
Match <input class="fx_parameter" data-bind="value: input.match" id="match" type="number">
Mismatch <input class="fx_parameter" data-bind="value: input.mismatch" id="mismatch" type="number">
</span>
</div>
</div>
<div class="row">
<div class="colW100"><label>Scoring in $g$:</label></div>
<div class="colW400">
<span class="group"> <!-- Microsoft Browsers will fallback on text-fields using following input type -->
Gap opening $\alpha$ <input class="fx_parameter" data-bind="value: input.baseCosts" id="base_costs" type="number">
Enlargement $\beta$ <input class="fx_parameter" data-bind="value: input.enlargement" id="enlargement" type="number">
</span>
<div class="group_hint">
<b>Hint:</b> <br />
For similarity maximization, <br /> match scores should be positive and all other scores lower.
</div>
</div>
</div>
<div class="row">
<div class="colW100">
<label>
<br />
Recursions:
</label>
</div>
<div class="colW600">
<span data-bind="text: $root.input.formulaP"></span>
<br />
<br />
<span data-bind="text: $root.input.formulaQ"></span>
<br />
<br />
<span data-bind="text: $root.input.formula"></span>
<br />
<br />
<br />
<span data-bind="text: $root.input.gapFunction"></span>
</div>
</div>
</div>
</div>
<h1>Output:</h1>
<div id="algorithm_output">
<div class="output">
<div class="main_output">
<table class="calculation_vertical">
<thead>
<tr>
<th>$P$</th>
<th></th>
<!-- ko foreach: input.sequence2 -->
<th data-bind="drawChar: [$data, $index()+1]"></th>
<!-- /ko -->
</tr>
</thead>
<tbody>
<!-- ko foreach: output.verticalGaps --> <!-- to get i-indexes = $parentContext.$index() -->
<tr>
<!-- ko if: $index() == 0 -->
<th></th>
<!-- /ko -->
<!-- ko if: $index() > 0 -->
<th data-bind="drawChar: [$root.input.sequence1()[$index()-1], $index()]"></th>
<!-- /ko -->
<!-- ko foreach: $root.output.matrix[0] --> <!-- to get j-indexes = $index() -->
<td class="selectable_entry"
data-bind="text: $root.output.verticalGaps()[$parentContext.$index()][$index()]"></td>
<!-- /ko -->
</tr>
<!-- /ko -->
<tr>
<th class="hint" colspan=100%> <!-- HINT: move colspan into hint-class when browsers are ready! -->
<small>
<b>Score:</b> -
</small>
</th>
</tr>
</tbody>
</table>
<br />
<br />
<br />
<table class="calculation">
<thead>
<tr>
<th>$D$</th>
<th></th>
<!-- ko foreach: input.sequence2 -->
<th data-bind="drawChar: [$data, $index()+1]"></th>
<!-- /ko -->
</tr>
</thead>
<tbody>
<!-- ko foreach: output.matrix --> <!-- to get i-indexes = $parentContext.$index() -->
<tr>
<!-- ko if: $index() == 0 -->
<th></th>
<!-- /ko -->
<!-- ko if: $index() > 0 -->
<th data-bind="drawChar: [$root.input.sequence1()[$index()-1], $index()]"></th>
<!-- /ko -->
<!-- ko foreach: $root.output.matrix[0] --> <!-- to get j-indexes = $index() -->
<td class="selectable_entry"
data-bind="text: $root.output.matrix()[$parentContext.$index()][$index()]"></td>
<!-- /ko -->
</tr>
<!-- /ko -->
<tr>
<th class="hint" colspan=100%> <!-- HINT: move colspan into hint-class when browsers are ready! -->
<small>
<b>Score:</b> <span data-bind="text: $root.output.score"></span>
</small>
</th>
</tr>
</tbody>
</table>
<br />
<br />
<br />
<table class="calculation_horizontal">
<thead>
<tr>
<th>$Q$</th>
<th></th>
<!-- ko foreach: input.sequence2 -->
<th data-bind="drawChar: [$data, $index()+1]"></th>
<!-- /ko -->
</tr>
</thead>
<tbody>
<!-- ko foreach: output.horizontalGaps --> <!-- to get i-indexes = $parentContext.$index() -->
<tr>
<!-- ko if: $index() == 0 -->
<th></th>
<!-- /ko -->
<!-- ko if: $index() > 0 -->
<th data-bind="drawChar: [$root.input.sequence1()[$index()-1], $index()]"></th>
<!-- /ko -->
<!-- ko foreach: $root.output.matrix[0] --> <!-- to get j-indexes = $index() -->
<td class="selectable_entry"
data-bind="text: $root.output.horizontalGaps()[$parentContext.$index()][$index()]"></td>
<!-- /ko -->
</tr>
<!-- /ko -->
<tr>
<th class="hint" colspan=100%> <!-- HINT: move colspan into hint-class when browsers are ready! -->
<small>
<b>Score:</b> -
</small>
</th>
</tr>
</tbody>
</table>
</div>
<div class="download_area">
<a class="table_vertical_download" href="#">Download Table P</a> <br />
<a class="table_download" href="#">Download Table D</a> <br />
<a class="table_horizontal_download" href="#">Download Table Q</a>
</div>
</div>
<div class="outcome">
<div class ="ancillary_output">
<table class="results_header">
<thead>
<tr>
<th>
Results <br />
<small>
You can select a result to get the related traceback.
</small>
</th>
</tr>
</thead>
</table>
<div class="results_with_scrollbar">
<table class="results">
<tbody>
<!-- ko foreach: $root.output.alignments -->
<!-- ko if: $index() < 10 -->
<!-- ko if: $index() == 0 -->
<tr>
<td class="selectable_entry selectable_entry_start">
<code data-bind="text: $root.output.alignments()[$index()][0]"></code> <br />
<code data-bind="text: $root.output.alignments()[$index()][1]"></code> <br />
<code data-bind="text: $root.output.alignments()[$index()][2]"></code>
</td>
</tr>
<!-- /ko -->
<!-- ko if: $index() != 0 -->
<tr>
<td class="selectable_entry">
<code data-bind="text: $root.output.alignments()[$index()][0]"></code> <br />
<code data-bind="text: $root.output.alignments()[$index()][1]"></code> <br />
<code data-bind="text: $root.output.alignments()[$index()][2]"></code>
</td>
</tr>
<!-- /ko -->
<!-- /ko -->
<!-- /ko -->
</tbody>
</table>
</div>
<table class="results_footer">
<tr>
<th>
<small>
<!-- ko if: $root.output.moreTracebacks -->
<b>Hint:</b> Only the first ten results are computed.
<!-- /ko -->
</small>
</th>
</tr>
</table>
</div>
</div>
</div>