UGENE Forum - common elements for plasmid annotations


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common elements for plasmid annotations (Read 7407 times)

Feb 6^th, 2012 at 10:25pm

dustman Offline
YaBB Newbies

Posts: 7

Is it possible to find a db with most common features to annotate plasmids (i.e. SV40/Lac/CMV promoters, SD sequence, etc.), especially sequences in .fa-format?

While .gb files are much easier to handle, elements still lack descriptors present in original .gb entry.

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Reply #1 - Feb 8^th, 2012 at 4:27pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

There is PlasMapper tool:
http://wishart.biology.ualberta.ca/PlasMapper/

Unfortunately, it is not yet integrated into UGENE, however we hope to provide similar features in future.

For now you can use various algorithms in UGENE to search for promoters regions, ORFs, restriction sites etc.

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