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All posts created by welkin

| posted 31 Oct, 2017 15:36
OK, I will add it.
Thanks!
Posted in: Request a new function on the SEA-PHAGES official listthymidylate kinase
| posted 31 Oct, 2017 15:36
YEs! That should be on the list. Thanks for pointing that out.
Posted in: Request a new function on the SEA-PHAGES official listqueuine tRNA ribosyltransferase
| posted 31 Oct, 2017 15:35
Isn't that on the list already? OR just needs to be put on there?
Posted in: Request a new function on the SEA-PHAGES official listphosphoribosyl transferase
| posted 31 Oct, 2017 15:32
Thanks for hunting this down!

But no, I don't think we will be putting signal sequences into annotation files.
Posted in: Functional AnnotationSignal peptides vs membrane proteins
| posted 31 Oct, 2017 15:31
Hi Jordan,
That's great that you found it; but no, we are not including attPs in annotations for GenBank.

Best,
Welkin
Posted in: Annotationannotating attP site
| posted 26 Oct, 2017 15:09
KAtie,
This looks like the executable is no longer in the DNA Master folder and it can't find the database files it needs. With the uninstalling/reinstalling did he accidentally drag it out somewhere?

Posted in: DNA MasterSSL error
| posted 26 Oct, 2017 14:44
Hi!
In order to add a new function to the official list, you need to present more of a case than "I found a domain match".

By more of a case I mean:
How large are known proteins of this type? Is the size of the protein you are investigating of similar size?
Are there conserved residues that are characteristic of this domain? Does your protein have them?
Are there normally other conserved domain present in conjunction with this domain? Does your protein have them?

In general, we don't like to put structural domains down as functional assignments, as too many proteins with a variety of functions can include them. However, if you are positive that your zinc-finger is DNA binding, then we can consider adding it if you have pursued the rest of the background.

Best,
Welkin
Posted in: Request a new function on the SEA-PHAGES official listZinc finger DNA binding domain/protein
| posted 09 Aug, 2017 15:17
Hi All,
I think we have decided that the best choices for now are:
PDB
pFam
CDD
SCOPe 70

The link to the new HHPred website is here, in case anyone has trouble finding it:
https://toolkit.tuebingen.mpg.de/#/tools/hhpred

However, as of 11am Eastern, on 8.8.2017, the site says it is undergoing maintenance. Hopefully it will be up again shortly!

Best,
Welkin
Posted in: AnnotationNew HHPred web site
| posted 07 Aug, 2017 16:26
Aug 2017. Full time position at a phage therapy company for a BS/MS with phage experience. Located in Gaithersburg, Maryland.
Edited 07 Aug, 2017 22:09
Posted in: General Message BoardBacteriophage Microbiologist Position
| posted 03 Aug, 2017 15:18
Sure. I wonder if there is a way to shorten the name and remain clear.
Posted in: Request a new function on the SEA-PHAGES official listmethyltransferase/glycosyltransferase