Team:Freiburg Software/User/Robots/Alignment

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<div style="width: 350px;"><p class="caption">Note: The display may slightly differ from this picture due to ongoing development.</p> </div>
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<h2>Local Alignment</h2>
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The Alignment Robot can also find local alignments using the Smith/Waterman Algorithm.
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Revision as of 19:14, 22 October 2010

Alignobot

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

With Alignobot you can compare sequences by creating global and local alignments. Alignobot can be found at alignobot@appspot.com. Before you start an alignment be sure that you have 2 sequences selected in the workspace.

Global Alignments

Alignobot finds global alignments using the Needleman/Wunsch Algorithm.

In the main menu you can either select the default distance function or specify your own. At this point the robot only supports one value for each substitution. Transition matrices will be available in a later version. Now click "Send" and Alignobot will calculate your alignment and display it:

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

Local Alignment

The Alignment Robot can also find local alignments using the Smith/Waterman Algorithm.