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All posts created by welkin

| posted 07 Jun, 2018 12:28
As a follow up from Graham:

How long is a piece of string?!
If [a new MPME] is 1 aa different, that is not enough for it to be MPME3. If it is a truncated version of MPME1, that does not make it MPME3. If there is a new MPME, full length with all of the features, and it is ~75% DNA identity to 1 and 2, then that would be 3.
Posted in: Cluster F Annotation TipsMPMEs--which one?
| posted 05 Jun, 2018 16:28
doesn't sound to me like you can clearly demonstrate DNA ds break repair. From Dave's post, all of those listed require a partner to actually do the repair.

I vote NKF for now.
Posted in: Request a new function on the SEA-PHAGES official listDNA double-strand break repair protein
| posted 05 Jun, 2018 16:26
I guess my questions here is what is the difference between BrnT and RelE, and can HHPred actually distinguish the difference between the two?
Posted in: Request a new function on the SEA-PHAGES official listRibonuclease toxin BrnT
| posted 05 Jun, 2018 16:23
So it sounds to me like the results are listing a number of things that we can't clearly distinguish from each other at this time. Is that true?
Posted in: Request a new function on the SEA-PHAGES official listDNA double-strand break repair protein
| posted 04 Jun, 2018 12:52
Is this the same as RepA? I think we have that already. IF not, how is it different?
Posted in: Request a new function on the SEA-PHAGES official list Replication initiator protein A
| posted 30 May, 2018 18:05
it is a sub-forum of this one.

https://seaphages.org/forums/forum/46/
Posted in: Functional AnnotationNicotinamide riboside transporter
| posted 30 May, 2018 17:26
sometimes I get those timeouts too. I usually wait five - to ten minutes and then try again. if it still doesn't work I email Dan.

Does it work now?
Posted in: AnnotationSubmission error
| posted 30 May, 2018 17:25
you are supposed to put "add function requests" on the "add a function forum".
smile

sounds like I forgot to put the function on the list when I did Wizard.
Posted in: Functional AnnotationNicotinamide riboside transporter
| posted 30 May, 2018 17:23
sounds like 4 might be an error– but there isn't any rule about where membrane proteins are in the genome. so 6 can stand.
Posted in: Functional AnnotationMembrane protein in DE phage
| posted 25 May, 2018 22:35
hi Joe,
you've got most of the nuances.

the idea with the "longest start language" is that there could be a conserved start upstream of the starts chosen in all the files. In our dataset, we've annotated phages as we sequenced them. So the start we selected when the phage was a singleton may not be the best choice. you could imagine a scenario in which we now have ten phages in the cluster, and they all have a longer start in common, even though we selected the shorter start for all the others because we didn't have enough comparative data.
So if you found such a start in the alignment, regardless of whether it was chosen most often in the GenBank files, it is probably time to do a reassessment, and reannotate all equivalent genes across the cluster.

does that make more sense?
Posted in: StarteratorHelp! I don't understand what this means!