Why is it "flipdna" not "revcompdna" or so?

[jan-glx]

Why is it "flipdna" not "revcompdna" or so?
Reverse complement seem to be the standard expression used in click-and-point and cli-based in-silico-molecular-cloning-software (e.g. pydna, Geneiuous, ugene)

[ponnhide]

Thank you for your comment.
In QUEEN, the operational function names ("cutdna", "modifyends", "flipdna", "joindna") have been determined to represent actual DNA sequence manipulations. For example, I believe the "flipdna" name is more appropriate than "revcompdna" when describing DNA inversion by site-specific recombination, such as Cre/loxP recombination.

I know that there are cases in which users may want to get a reverse complementary sequence regardless of experimental DNA sequence manipulations. However, I did not use a name like "revcompdna" because it is unsuitable for the QUEEN concept.

[jan-glx]

I really like how QUEEN tries to abstracts all the stuff we can do in the lab into a few operations and how it enables reproducible, modifiable and appealing descriptions of those.

The following might appear pedantic, but I'd really like to fully understand what a QUEEN objects and operational functions are meant to represent.

Flipping or reverse complementing an actual dsDNA molecule would be a null operation (It's the same molecule no matter which strand you define as top strand).

QUEEN operational functions seem to operate on dsDNA sequences i.e. joindna requires the sequences to be oriented correctly (it doesn't find the matching end like a ligase would).

I'd argue that flipdna doesn't represent something like DNA inversion by site-specific recombination (as it would then need to operate only on a subset the sequence) but that it rather really only changes which strand is considered the top strand (for visualization and for defining which site the other operations act on). Thus I see "reverse complement" as a more appropriate name.

Do you have plans to provide higher level functions, representing reactions like PCR, in addition to the low level interface?

[ponnhide]

QUEEN operational functions seem to operate on dsDNA sequences i.e. joindna requires the sequences to be oriented correctly (it doesn't find the matching end like a ligase would).

I could understand your argument from this statement. As you pointed out, the current joindna function requires orient correctness and does not match the DNA sequence manipulation in molecular cloning. OK, I will consider operational function names and implementations more to represent their actual functions.

Do you have plans to provide higher level functions, representing reactions like PCR, in addition to the low level interface?

At present, I don't have such a plan because QUEEN is designed to represent various molecular cloning processes by combining operational functions. However, recently, I've thought that such high-level interfaces may be required to promote the use of QUEEN in the life science community.

[jan-glx]

Happy to see that you added such high-level functions in 1.2 🤩