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All posts created by welkin

| posted 07 May, 2019 19:50
Hi All,
The frameshift should be in close proximity to the C-terminus of the G protein; the GN-GK one is simply too far away.
We probably should look at all the CZ4s and see if there is a consensus.

Posted in: Frameshifts and IntronsCluster CZ4 Frameshift
| posted 30 Apr, 2019 15:07
Depends on how humid the air is. Under vaccuum and with dessicant, months; under humid conditions, maybe a few days tops.
Posted in: Phage Discovery/IsolationEM Sample Stability
| posted 29 Apr, 2019 14:57
I think this has to be a minor tail protein; otherwise there won't be enough proteins to make up the tail tip.
Posted in: Request a new function on the SEA-PHAGES official listAlpha-L-arabinofuranosidase B?
| posted 26 Apr, 2019 18:32
Hi Dave,
Sounds like it to me.

Posted in: Functional Annotationthymidylate synthases versus dihydrofolate reductases
| posted 25 Apr, 2019 22:33
Hi Veronique,
How long is the protein, and how many other minor tail proteins have you identified already?
Posted in: Request a new function on the SEA-PHAGES official listAlpha-L-arabinofuranosidase B?
| posted 25 Apr, 2019 22:25
It is OK to indicate on your coversheet which scoring matrix and spacing matrix you used, as long as you don't change it on a per gene basis. Z-score and final score should still be included with every gene.
Yes/no indicates if it is the best score or not, as compared to the other choices for that gene.

Edited 25 Apr, 2019 22:32
Posted in: DNA MasterRBS Data
| posted 19 Apr, 2019 21:52
The capsid, scaffolding, and protease are fused into a single gene in the EEs and should be annotated as "major capsid and protease fusion protein"
Edited 25 Apr, 2019 22:27
Posted in: Cluster EE Annotation Tipscapsid and protease fusion
| posted 18 Apr, 2019 13:09
Hi Sally,
I thought M23 was on the list already– go head and use it. and I don't think we can be more specific and use M23B without better data.

Posted in: Functional AnnotationLysin A in Rhodococcus phage
| posted 17 Apr, 2019 17:17
As of April 2019, we have been unable to identify the major capsid protein, and so you do not need to include it in your annotation.
Posted in: Cluster EK Annotation Tipsmajor capsid protein
| posted 17 Apr, 2019 13:22
Hi Sally– Debbie and I spoke offline a bit, and we are going to amend the "RexA" only function. We try hard not to just use the protein names because students get stuck in the alphabet soup when there is no additional information (RecA and RexA are very different, no?)

So I've added a bit to the designations:

RexA family abortive infection protein
RexB family abortive infection protein

Posted in: Functional AnnotationRexAB systems