Restriction mapping using webcutter
One common task in the analysis of nucleotide sequences is that of searching for restriction sites.
The webcutter tool allows restriction maps of nucleotide sequences to be generated in a flexible fashion, producing a nicely formatted output.
You may have noticed that BCM has webcutter built in and a number of other sites offer webcutter services. However, we will visit the faster site hosted by the creator of the webcutter tool.
We will look at a restriction analysis of the glutamate racemase gene that we retrieved from GenBank (or EMBL).
Click here to launch Web cutter. The web cutter home page will appear, containing a number of text fields that allow you to tailor your restriction analysis.
Webcutter is very flexible in the sequence entry method. In addition to cut and paste, you can upload the sequence from your computer (on floppy or Hard disk) or you can retrieve them directly from the GenBank database.
Since we already have our sequence we’ll go for the simple cut and past approach
Step 1: Copy the FASTA formatted glutamate racemase sequence from the Word document in which you pasted it (or click here to get it).
Step 2: Paste the sequence into the box labelled ‘Paste the DNA sequence into the box below’.
There are a number of options you can change simply by clicking the appropriate option buttons below the sequence entry box.
It’s also possible to select both subsets and individual enzymes.
For the sake of simplicity we will leave them all on the default settings.
Click on the grey ‘Analyze sequence’ button at the bottom of the page. (show me)
You will be presented with a graphical representation of you sequence with the restriction sites printed alongside the sequence and a table that lists the position of the target sequences in your sequence.
Enzymes that are commonly used for cloning are highlighted in colour – e.g. The SmaI site in our sequence is orange.
This output can also be cut and pasted in to Word if you desire.
(Hint - when handling sequence in Word it lines up best if you change the font to Courier New, size 8)