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All posts created by welkin

| 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.
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".

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!
| posted 25 May, 2018 14:53
Hi Ken,
Either is fine. The computer program will truncate whatever you put in the "first name" column down to a single initial.

Thanks for asking.
Posted in: Notes and Final FilesAuthors file
| posted 23 May, 2018 13:28
Hi MArie,
Do you have any BLAST results for lysins in the Mycobacteriophages? The lysin A domains were extensively characterized by Kim Payne in Graham's lab.
My favorite way to assign the domains is to align the gordonia lysins with the phages from the Payne and Hatfull paper in 2012 about lysins. Kim really did that bench work, so if you have sequence alignment to those domains, you can feel confident about being more specific.

Posted in: Functional AnnotationLysins in Gordonia
| posted 22 May, 2018 15:34
Hi Nikki,
You are right— one amino acid off means we will stay with MPME1.

Posted in: Cluster F Annotation TipsMPMEs--which one?