Annotating shorter than 600 bp control region

[Phismil]

Dear Guanliang
Thank you for maintaining and updating the repository.
I have a question regarding the annotation of the control region :
Is there any solution to report the annotation of putative control regions that are shorter than 600 bp, which is the minimum length required for reporting putative control regions based on the MitoZ paper?
Thank you in advance

[linzhi2013]

Hi Phismil,

In MitoZ paper,

We further annotate the putative control region in the case that the remaining interval region has a length ≥ 600 bp ([48] and all its PCGs, tRNA and rRNA are fully recovered.

"600 bp" is an arbitrary cutoff. We only consider annotating "the putative control region" when all other genes are recovered.

Do you mean that some species have control regions less than 600 bp? If this is case, I can add an option to allow users to change this value.

Cheers

[Phismil]

Dear Guanliang
Thank you for your kind response.
Yes, you are correct. Some species of invertebrates have a control region that is slightly shorter than 600 bp and it has been speculated that some might have more than one control region.
The addition of this option will be extremely useful and highly appreciated. I am using the singularity container, and I guess it might need some time for this option to be available in the container.
Cheers

[linzhi2013]

Thanks, @Phismil!

It would be great if you can provide a few publications about "some might have more than one control region." I'm interested in having a look at them.

[Phismil]

Hi,
As a mainly vertebrates geneticist, my knowledge is not the most updated, but I remember that we discussed this paper in a workshop. We have been told that it is very common in plants as well.
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-394
Cheers

[linzhi2013]

Hi Phismil ,

Thanks for it!!

[scintilla9]

Hi @linzhi2013

Are there any updates or new features related to this issue?
I have a similar requirement for shorter control region.

Thanks!