Team:Freiburg Software/User/Robots/REBase

From 2010.igem.org

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<h1>REBase Robot</h1>
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<div align="center" class="box_robot">
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<img src="https://static.igem.org/mediawiki/2010/5/5a/Freiburg_10_software_Internals.png" width=100/>
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<p class="main">
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This page describes the use of the REBase Robot. If you would like to know how the algorithm works internally please click <a href="#Internals">here</a>.
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<p class="main">
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Using REBase robot, user can find where in his sequence restriction sites attach to the sequence and also where the cut the sequence. REBase robot can be found at resenzymes-beta@appspot.com<br>
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Before you start finding the details about the restriction sites using this robot, make sure that you have a sequence selected in the workspace.</p>
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<iframe src="http://player.vimeo.com/video/16210395" style="width: 510px; height: 287px; float: left; margin: 15px 0px 45px 20px;" frameborder="0"></iframe>
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<h2>Enzyme Selection</h2>
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<p class="main">
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This robot first identifies if the <a href="http://rebase.neb.com/rebase/rebase.html">Restriction Enzymes Database</a> is updated. If so it updates the local restriction enzymes database. Then it provides a list of enzymes to select from.
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<div align="center" style="margin: 10px 10px 10px 10px; width: 300px;">
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<img src="https://static.igem.org/mediawiki/2010/c/c8/Freiburg_10_Software_Rebase_Parameters.png" />
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<h2>Restriction Enzymes identification</h2>
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<p class="main">
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REBase robot searches for the entry pertaining the enzyme selected by the user in the local database. It then identifies the sequence and cut details of the enzyme. Then it goes through the sequence and finds all occurrences of the selected enzyme in the sequence. The output of the REBase robot is similar to the the following image. It displays the original sequence, followed by the sequence highlighted at Restriction Enzymes positions.
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<div align="left" style="margin: 10px 10px 10px 10px; width: 600px;">
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<img src="https://static.igem.org/mediawiki/2010/2/21/Freiburg_10_Software_Rebase_Screen.png" width=750/>
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<div style="width: 600px;"><p class="caption">Note: The display may slightly differ from this picture due to ongoing development.</p> </div>
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In future, we plan to extend the functionality to let user select more than one Restriction enzymes at once.
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<h2 id="Internals">Brief Overview of Algorithm</h2>
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<p class="main">
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This robot first identifies if the <a href="http://rebase.neb.com/rebase/rebase.html">Restriction Enzymes Database</a> is updated. If so it updates the local restriction enzymes database. Then it provides a list of enzymes to select from.<br />
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It then simply traverses through the sequence to check if the sequence contains any of the selected sequence.<br />
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When it finds it indicates the start, stop position and the cut of the enzyme.
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Latest revision as of 00:15, 27 October 2010

REBase Robot

This page describes the use of the REBase Robot. If you would like to know how the algorithm works internally please click here.

Using REBase robot, user can find where in his sequence restriction sites attach to the sequence and also where the cut the sequence. REBase robot can be found at resenzymes-beta@appspot.com
Before you start finding the details about the restriction sites using this robot, make sure that you have a sequence selected in the workspace.

Enzyme Selection

This robot first identifies if the Restriction Enzymes Database is updated. If so it updates the local restriction enzymes database. Then it provides a list of enzymes to select from.

Restriction Enzymes identification

REBase robot searches for the entry pertaining the enzyme selected by the user in the local database. It then identifies the sequence and cut details of the enzyme. Then it goes through the sequence and finds all occurrences of the selected enzyme in the sequence. The output of the REBase robot is similar to the the following image. It displays the original sequence, followed by the sequence highlighted at Restriction Enzymes positions.

Note: The display may slightly differ from this picture due to ongoing development.

In future, we plan to extend the functionality to let user select more than one Restriction enzymes at once.

Brief Overview of Algorithm

This robot first identifies if the Restriction Enzymes Database is updated. If so it updates the local restriction enzymes database. Then it provides a list of enzymes to select from.
It then simply traverses through the sequence to check if the sequence contains any of the selected sequence.
When it finds it indicates the start, stop position and the cut of the enzyme.



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