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All posts created by welkin

| posted 19 Jul, 2017 15:06
hi Steve— send data! DNA Master file, screenshots?

I also like to get a sense of exactly what the putative functional match is before I use something specific: here is a nice description on Ocr and its characteristics that are essential for functionality.

https://academic.oup.com/nar/article/40/16/8129/1031862/Exploring-the-DNA-mimicry-of-the-Ocr-protein-of

Edited 19 Jul, 2017 15:14
Posted in: Functional AnnotationGene with homology to T7 Ocr gene
| posted 07 Jul, 2017 19:17
Dan, is it worth doing a Sanger run across the area to resolve?
Posted in: Gene or not a GeneGene split in 2
| posted 07 Jul, 2017 19:16
Yep, we can add officially. give me a phage name and gene number.
Posted in: Functional AnnotationFunctions not on the approved list
| posted 08 Jun, 2017 15:27
I agree! Stick to NKF.
Posted in: Functional Annotation Ead/Ea22-like protein
| posted 06 Jun, 2017 13:00
Sounds fine.
Posted in: Functional AnnotationPhosphoesterase with intein domain
| posted 06 Jun, 2017 12:59
I don't know what an Ead/Ead22 -like protein is. Can you elaborate? Does it make sense in the context of phage biology?
Posted in: Functional Annotation Ead/Ea22-like protein
| posted 06 Jun, 2017 12:58
do both parts have good coding potential?
Posted in: Gene or not a GeneGene split in 2
| posted 19 May, 2017 16:36
Found a ParB in a Cluster B phage? As far as we know, the ParB domain containing gene in the Cluster B phages is not a true ParB protein. We have been unable to make lysogens from Cluster B phages, and so we do not think this is a Partitioning Protein like the ParAB system found in some Cluster A phages. As a general rule of thumb, we never assign "ParB" as a function to a gene in which we can not also identify a ParA.
If your "ParB" has really good evidence, you may assign it the function of "ParB-like nuclease domain".
Edited 01 Mar, 2018 15:41
Posted in: Cluster B Annotation TipsParB
| posted 19 May, 2017 16:32
Can't find lysin B? No worries! Cluster B2 phages do not have a lysin B!
Edited 20 Aug, 2018 15:56
Posted in: Cluster B Annotation TipsLysin B
| posted 05 May, 2017 16:11
You need to include the amino acid and the anticodon for tRNAs for GenBank ready minimal files.
If both programs are undetermined, you can use "tRNA other" and the anticodon. If tRNA scan has made up its mind, and ARagorn hasn't, use the tRNA scan decision.
Posted in: tRNAsundetermined tRNA's