Rho- vs. rho-independent

[stianale]

Hi, nice software

Does BacTermFinder not annotate predicted terminators as Rho-dependent or Rho-independent?

Kind regards

[stianale]

It has been two weeks since I asked this question, by the way

[AminTaheri23]

Hello Stianale,

Differentiating between factor-depedent (aka rho-dependent) and intrinsic terminators is outside of the our scope for BacTermFinder 1.

However, we are working on BacTermFinder 2 with this ability in mind. I'll let the researchers of that project know if their work is published or not.

Quick question, what use case you have in mind if BacTermFinder supports this feature?

Thanks,
Amin

[stianale]

Hello Stianale,

Differentiating between factor-depedent (aka rho-dependent) and intrinsic terminators is outside of the our scope for BacTermFinder 1.

However, we are working on BacTermFinder 2 with this ability in mind. I'll let the researchers of that project know if their work is published or not.

Quick question, what use case you have in mind if BacTermFinder supports this feature?

Thanks, Amin

Not sure of use case, but was thinking that it would be interesting to be able to distinguish the types. As of now it is just agnostic to type, so it is different to really compare to other predictors exlusively for Rho-independent terminators, for example.

Kind regards,
stianale

[stianale]

Hello Stianale,

Differentiating between factor-depedent (aka rho-dependent) and intrinsic terminators is outside of the our scope for BacTermFinder 1.

However, we are working on BacTermFinder 2 with this ability in mind. I'll let the researchers of that project know if their work is published or not.

Quick question, what use case you have in mind if BacTermFinder supports this feature?

Thanks, Amin

I am working on an analysis of genomic repeats and BacTermFinder in which distinguishing between the types of terminators would be helpful. Can I quote you, as a BacTermFinder developer, on this: "However, I could not establish the degree to which [my repeats] are present in Rho-dependent terminators, as BacTermFinder does not yet distinguish between types of predicted terminators, although this is planned for future versions of the software (personal communication with BacTermFinder developer)"?

Kind regards,
stianale

[AminTaheri23]

Hello @stianale,

I'm sorry for not getting back to you sooner. Yes, you can quote that and even reference this GitHub Issue #4.

Thanks,
Amin