Unique restriction sites in two sequences - (Apr/11/2006 )
I am doing restriction digestion and ligation type of cloning. To check that the insert is situated at the right place in the vector, I am planning to cut the vector at unique restriction site and the insert at unique restriction site so that from the resulting bands I would get information if cloning has worked before I go ahead to the next step.
I can very well find unique restriction sites within each sequence by putting it seperately in DNAstrider but I wondered if there is any program or on-line application where I can paste both the sequences and run to check if there is any unique site which is available in vector and not in the insert and vice-versa.
I get totally lost otherwise if I try to do one by one.
You can upload your sequences to http://workbench.sdsc.edu and use the nucleic tools and there is an enzyme sites search.
There is an excelent and free program called ApE:
Open one of your sequences and choose from the Menu Enzyme->Enzyme selector
In the drop down box chhose "unique" and click on "Select".
All unique enzymes will be labeled red. Close this window and open your second sequence.
Open the Enzyme Selector window again and look at the red enzymes you labeled for the first sequence. In parathesis near each enzyme name you will find the number of times it cuts your second sequence.
I use this one
I just paste in the two sequences contiguously, as they would be in the final cloned plasmid, and look for single cutters