Hi, I'm back to doing cloning, and so have found two bugs when using PCR in silico.

First, if I try to copy a primer sequence from LibreOffice Calc spreadsheet (a very common way of storing primer sequences), I can not paste it into the primer text boxes. However I can paste it into the Search field, then copy it from there and paste. Clearly, something is wrong with the primer text boxes...

Secondly, if my primers have a 5' sequence not complementary to the template, the programme won't find any products. I think it used to work before, and I guess that's why there is a field with 3' perfect match - that nucleotides on the 5' don't have to match. However it doesn't work.

I am running the latest ugene (1.24.2, as a binary package which I start from the command line) on Ubuntu 14.04. Thanks!

Hello, Ilya!


Quote:

First, if I try to copy a primer sequence from LibreOffice Calc spreadsheet (a very common way of storing primer sequences), I can not paste it into the primer text boxes. However I can paste it into the Search field, then copy it from there and paste. Clearly, something is wrong with the primer text boxes...

Yes, indeed, the copied cell also contains the new line character which is rejected by the text box validator. We will fix it in UGENE 1.26 (version 1.25 is already under development).


Quote:

Secondly, if my primers have a 5' sequence not complementary to the template, the programme won't find any products. I think it used to work before, and I guess that's why there is a field with 3' perfect match - that nucleotides on the 5' don't have to match. However it doesn't work.

Yes, in the current UGENE version you should increase the number of mismatches for each primer to find the product. It was like that since the feature implementation. The '3' perfect match' option additionally disallows mismatches in the specified number of characters from the 3' end.

We may change this feature in future - allow one to specify characters on the 5' end separately, help to add the required restriction site to the end and change a primer visualization in the Sequence View.

Thanks for the explanation, Olga!