A question we get asked all the time–and I see on mailings lists with about a twice/year frequency–is where can I look at the restriction sites in my sequences? I’m going to mention a few that I know about, but if anyone has other favorite tools or spots, do let us know in the comments.
UCSC Genome Browser: if you look in the browser in the “Mapping and Sequencing” Track groups area there is a menu called Restr Enzymes. I have turned this track on, and turned off some other default tracks, and created a “Session” to show you exactly how this can look. I picked a small gene for the example. Load my session: http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Mary%20Mangan&hgS_otherUserSessionName=restriction_enzymes
You can see the sites in Ensembl, too. From that UCSC session I provided you can click the link in the blue navigation area at the top of the UCSC page to go to the exact same region in Ensembl. In the “Detailed View” section at Ensembl you can see menus for “Decorations” and other display features. In Decorations you can check the box for Rest. Enzymes to see them on your viewer.
However, there may be times where your sequences is different from genomic, or not available in a species browser, and sometimes you just want another type of viewer. You might try PlasMapper (http://wishart.biology.ualberta.ca/PlasMapper). I took the same sequence from the browsers (the Casp-1 gene) and put the FASTA sequence in, and created a really quick map. It also gives text output if you prefer. It can add a display for some handy features that you might have on plasmids or constructs like promoters or affinity tags. Takes only a few seconds, a very handy little freely available tool for you to know about. I know it isn’t new, but it is such a common question for us that we thought we would mention it.
Dong, X., Stothard, P., Forsythe, I.J., Wishart, D.S. (2004). PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Research, 32(Web Server), W660-W664. DOI: 10.1093/nar/gkh410