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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> common elements for plasmid annotations https://forum.ugene.net/forum/YaBB.pl?num=1328541958 Message started by dustman on Feb 6^th, 2012 at 10:25pm

Title: common elements for plasmid annotations
Post by dustman on Feb 6^th, 2012 at 10:25pm

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.

Title: Re: common elements for plasmid annotations
Post by Konstantin Okonechnikov on Feb 8^th, 2012 at 4:27pm

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.