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To load sequences to ExpertDiscovery click on the New ExpertDiscovery Document toolbar button:

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The following dialog will appear:

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Load the sequences you want to analyze by choosing any file with a sequence or multiple sequences. Positive sequence base contains a regulation object you are interested in. Negative sequence base doesn't have it. You also may generate negative sequences automatically. ExpertDiscovery will extract complex signals which reflect a structure of your regulation object. The more sequences you provide the better will be result. Click on the Next button. The following dialog will appear:

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Here you can to load markups for the sequences. Markup is an annotation of a sequence with elementary signals. Markup gives information where elementary signals are located in the sequences. Complex signals will be build from the elementary signals and operations applied to them. Load markup for your sequences in specified XML format or genbank format. To skip this step click on the Cancel button. To call this dialog again click on the Load markup toolbar button.