UGENE Forum - Can I link Ugene to a local database?

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Can I link Ugene to a local database? (Read 6065 times)

Dec 14^th, 2012 at 7:01pm

overthere Offline
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Hi I was wondering if its possible to link Ugene to a local database of primers, plasmids etc, such as is possible in Gentle (gentle.magnusmanske.de/). If not this would be a really useful feature to make UGene suitable for day to day molecular biology use as opposed to genome analysis.
Thanks
overthere

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Reply #1 - Dec 17^th, 2012 at 5:35pm

Yuriy Vaskin Offline
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As I understand, in Gentle you need to create the database file first before linking, right? Can Gentle read any other db file created by other tools?

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Reply #2 - Dec 17^th, 2012 at 7:26pm

overthere Offline
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Gentle comes with a built in database that you can add to or can be pointed at external MySQL databases.

Just to be clear I'm not asking if I can transfer a Gentle database across. I'm wondering if a similar functionality exists in UGene at the minute, I can see how to connect to large external repositories but not the more 'lab scale' ones that are useful for keeping track of primers ,plasmids etc.

And finally thanks for the great software!

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Reply #3 - Dec 18^th, 2012 at 2:10pm

Yuriy Vaskin Offline
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Thanks for your suggestion!

For now UGENE uses ordinary files to load and write data for users. It actually stores all sequences in the embedded database. But it's like an inner representation of the data which is almost impossible to access outside.

We'll think about how to build these databases with sequences in a convenient way.

But for now have a look at our way to deal with enzyme files http://ugene.unipro.ru/documentation/manual/plugins/restriction_analysis.html&nb...; (Using Custom File with Enzymes) and projects http://ugene.unipro.ru/documentation/manual/basic_functions/working_with_project...

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