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j5 Golden Gate Assembly and Device Manager

Does anybody know if the j5 assembly system from the JBEI is still active?

http://j5.jbei.org/

I am trying to create a Golden Gate assembly strategy for a set of DNA sequences. However, when I send a request to the server to produce the strategy, I just get a loading bar and the process never completes, despite being left for an hour.

Any idea why that might be?

Alternatively, does anybody know of any tools for producing DNA assembly strategies with the Golden Gate method?

synthetic-biology assembly golden-gate dna
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updated by Ram Ram • written by willemveerman • willemveerman

1 answer

Hi Willem,

j5 is very much still active (as you know now).

The reason that the combinatorial j5 runs you submitted through DeviceEditor took a long time was because the source sequences for your parts were whole genome sequences, which makes running BLAST during the primer design and assembly junction design process take much longer.

Furthermore, running long (time-wise) DNA assembly designs can be problematic, especially from outside of the U.S., because to get a response you will need a perfectly persistent internet connection.

The commercial grade version of the j5 software, available at:

https://www.teselagen.com

is not subject to this persistent internet connection requirement, as it will save your previous j5 run results so that you can leave the site safely without jeopardizing your access to the run.

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updated by Ram Ram • written by hillson • hillson

Hi Nathan,

Yes, I do now know this - my runs successfully came through.

Was going to write a post here so that users did not get misled. I was on a home connection which kept dropping out, back on campus it works just fine.

Thanks again!

I'll leave the post here so that anyone who stumbles across it is not misinformed.

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updated by Ram Ram • written by willemveerman • willemveerman

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