Example:

 

How to use the EMBOSS programs to find restriction sites and fragment lengths in plasmid vector pGT4.

Allow circular DNA
Show fragment lengths

Find single cutters
Sort output alphabetically

 

Go to http://emboss.bioinformatics.nl/

In the left pane: scroll down till the nucleic Restriction group

 

 

 

and choose restrict:

 

 

When the restrict page is open, paste the pGT4 DNA sequence in the To enter the sequence manually field

 

 

This is what you get:

 

 

Scroll down, and leave all options default except

 

 

After changing the default Show fragment lengths? No to Yes,
click the Run restrict button.

 

 

This is what you see first:

 

 

Don't worry, just scroll down untill you see this:

 

 

which shows you, that pGT4 (3793 basepairs) has a (apparently unique) BamHI restriction site at position 1180 (it is GGATCC from position 1180 to 1185) and an (also unique) EcoRI restriction site at position 1557 (it is GAATTC from position 1557 to 1562).

A digestion with both enzymes gives fragments of 3416 and 377 basepairs.
(note: Sometimes the EMBOSS restrict output gives unexpected results. More..)

 

If you would like to  find all single-cutters for pGT4 (restriction enzymes that have only one recognition site in pGT4) do the following:
leave or fill-in all in the Comma separated enzym list, and set the Minimum and the Maximum cuts per RE to 1, to get a complete list with unique sites in pGT4, like this:

 


 

To get a list with the single-cutters in alphabetical order, set the option in the Output section, like this: