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Restriction sites, complement searching (Read 3606 times)
Apr 1st, 2012 at 6:50am

abiologystudent   Offline
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Hi there,

How do I search for the complement of a restriction site in my sequence? Currently, Ugene is only finding the site on the 5' strand and not the reverse site on the 3'. I've spent a good hour attempting to do this, what have I missed here?

Thanks in advance,

Thomas
 
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Reply #1 - Apr 2nd, 2012 at 7:55pm

Konstantin Okonechnikov   Offline
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Posts: 173
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Hi Thomas,

By default UGENE searches for restrictions sites on both strands. However for enzymes with palindromic recognition sequences the result is always shown on direct strand.

For non-palindromic enzymes strand is selected according to the restriction site location. Try for example searching for AciI site.

Do you want to filter the results only to specific strand?
 
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