You may find this one useful: http://www.addgene.org/analyze-sequence/ The free to use web-based software analyzes your sequence and compares it to known promoters, terminators, antibiotic resistances and so on. At the end you get an annotated plasmid or sequence you can export as GeneBank file. If you need a sequence editor I can recommend Geneious (http://www.geneious.com/) which is slightly cheaper than VectorNTI but has also a lot of features including virtual cloning. Sadly, VectorNTI once was free to use for academics but now it is not anymore.

I use Clonemanager program

I would also strongly recommend Serial Cloner. You may also want to consider pDRAW to generate your vector maps. It has limited analytical capabilites compared to Serial Cloner but is very useful to generate clearly laid out plasmid maps and its very straight forward to use. And its also for free - have a look at http://www.acaclone.com/

Yet another, free, web-based option is plasmapper, http://wishart.biology.ualberta.ca/PlasMapper/ It gives a nice map and adds identified sequence motifs and restriction sites.

I used to use Vector NTI free version. However, I found SnapGene viewer and I like it better than vector NTI. It's free download.

Thanx a lot everybody for your positive and overwhelming response...

I used to use Vector NTI. However, I found VectorFriends and I like it better than vector NTI.

It's free for academic researchers and can be downloaded at http://www.vectorfriends.com

Clone manager is a perfect one, ALso NTI.

I like SnapGene, but its not for free (just the 30-day trial version), SnapGene Viewer is for free, but it has limited functionality- you cannot do in silico gene cloning in it

You can try APE. It is free and very good. http://biologylabs.utah.edu/jorgensen/wayned/ape/

I don't want to sound like I'm tooting my own horn but I've written one over the past year or so and have just recently placed it online. It's a work in progress but it's 100% free and allows you to search (and add, delete/modify) from a library of sequences (simple, degenerate, gapped), both DNA and amino acid. You can run a virtual gel, do restriction digests, and more. I'm updating it and adding features frequently. I also appreciate constructive feedback and bug reports!

You can find it at:

http://plasmidplotter.blogspot.com/

(I should make it clear that this is something I've made in my free time and is not affiliated with my university)

I tried APE (MacVersion) and worked wonderful! I recommend it. There is also a Windows version.

I am a huge fan of Snapgene. (http://www.snapgene.com/) There is a free 30 day trial of the full version, but "Snapgene Viewer"--which has most of the functions you're looking for (automatically annotates various features, allows you to see/choose restriction enzymes, generates plasmid maps, and much more...)--is completely free. Full disclosure: I have not yet tried many of the alternatives, but that is mostly because I am so happy with Snapgene.

 You can do this on Benchling. Just drop your sequence file in or paste in the bases. Customize what appears on the map (e.g. annotations, primers, cut sites) and export it as a PDF or SVG when you are done, like this example: https://benchling.com/s/bo6DLuaG

https://benchling.com

Joining the discussion a bit late. I really like ApE as several users recommended above. Really basic but does the job. However I recently changed my laptop and it is now very slow and ineffective. Wonder if anyone has had the same issue?

is ape http://biologylabs.utah.edu/jorgensen/wayned/ape/ closed or moved ?

Try WebDSV, it is a basic molecular cloning software providing all the required functionalities – DNA sequence editing, feature management, and map drawing. It works the same on all platforms (Windows, Mac, Linux) and uses the universal GenBank file format.

http://www.molbiotools.com/WebDSV/index.html

How about Snap Gene viewer ? You can try

Try www.benchling.com

Not free, but on the Windows machine I use Clone Manager (www.scied.com)