Two ending sequences of D1D1 about cims-cyanobacterial-its-motif-slicer

[nlabrad]

Just to clarify, is this an issue with the ending of the d1d1?
This is what I understand is happening:

There are two possible endings of d1d1, the correct one is the second one, but the script is picking up the first one.
Should it ALWAYS pick the last one?
@callmcgovern @phycologia

[phycologia]

@nlabrad I'm not sure, cause I guess it depends on where else the supposed ending motif comes up.... I encountered the same sort of thing (a possible D1 ending and then another possible ending about 10 bp further away) when I was first annotating the GARN sequences. Supposedly the base right after the last D1 base will be a G--that's how I decided to go with the second possible ending in my case.

[aimeee05]

Yeah when two possible endings were close together I usually had to go with the second one, I don't want to say this is always the case because I'm sure there are always exceptions but it seemed like when the D1D1 strand was a little shorter the second D1D1 ending ended up lengthening the sequence and gave the right structure.

[nlabrad]

I think we have a proposed solution in the works.
Now it finds all the possible d1d1 endings and presents them to the user for them to do as they wish. There is no interactivity yet like "hey we found 2 which one you want", I don't know if that's something we want. @callmcgovern? I figure you don't really know which one you need until you fold them, so they wouldn't know anyway.

[nlabrad]

The new version is under the "new algorithm" branch.

[nlabrad]

@aimeee05 I think this has been fixed. It now searches for all the possible d1d1 endings within the first 150 bases. This limit is defined by us, hardcoded, and because that's what I was told to do lol, but if it needs to be different we can change it.