Support degenerated sequences during PCR In Silico

It must be possible to work with primers that have "Extended DNA" alphabet:

1. To add them into the primer library.
2. To input them on the "PCR In Silico" tab.
3. To use them in the PCR workflow samples.

The original sequence, used for simulating a PCR process may also be of the "Extended DNA" alphabet.

Comparison of characters between a primer and a sequences must be done as follows. The characters are considered the same:

• If they are the same E.g. B=B.
• If character from the "Standard DNA" alphabet corresponds to one of the possible values of a character from the "Extended DNA", e.g. "B=C".

Check out the "Extended DNA" alphabet in the UGENE source code. It must be the following:

B=(C,G,T), D=(A,G,T), H=(A,C,T), K=(G,T), M=(A,C), N=(A,C,G,T), R=(A,G), S=(G,C), V=(A,C,G), W=(A,T), Y=(C,T);

See also: http://primerdigital.com/tools/pcr.html