Since freeware like PlasMapper annotate genomes up to 20 kbp I could not find a reliable tool for a graphical analysis of my 80 kB plasmid. I performed RAST annotation already which was quite successful but I could not figure how to make a nice graphics of my large plasmid. Someone having an advice?
I've never tried 80kB, but I'm very partial to Serial Cloner (100% free), which can pull basic annotations off the web and has a lot of other neat tools. Sometimes it doesn't read all the different filetypes, so when I download from addgene or get a sequence from someone else, I sometimes have to convert to a different filetype using SnapGene Viewer. SnapGene can do some functions too, but is limited unless you want to pay.
http://serialbasics.free.fr/Serial_Cloner.html
http://www.snapgene.com/products/snapgene_viewer/
I have never tried it with such a big plasmid but I always use:
http://wishart.biology.ualberta.ca/PlasMapper/
We use SnapGene and we pay for it! I tried import the phage lambda sequence as a genbank file. That's close to 50Kb. It processed it like a charm. The auto-detect feature was also very fast.
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