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byrumc@cofc.edu posted in How to cite...version number for Phamerator

cdshaffer posted in Whole phage starterator reports

cdshaffer posted in How to cite...version number for Phamerator

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Shallee Page posted in tailproteinsunwinding?

All posts created by lhughes

| posted 01 Jul, 2017 21:17
lhughes avatar
lhughes
A lot of the BD1 Streptomyces phages have a "dNMP kinase" that isn't on the official list. HHPRED matches are written as "deoxynucleoside monophosphate kinase" so I thought written out might be better? Can we add officially?
Posted in: Functional Annotation → Functions not on the approved list
| posted 01 Jul, 2017 20:56
lhughes avatar
lhughes
The official list has RuvC resolvase, but all my HHPRED hits for some of our genes are hitting Holliday Junction Resolvase (which I am assuming, hopefully correctly, is really the same thing by a different name). None of the hits use the RuvC resolvase term.

Should I stick with RuvC resolvase or would it be better to start using Holliday junction resolvase?

Lee
Posted in: Functional Annotation → RuvC resolvase vs Holliday Junction Resolvase
| posted 20 May, 2017 16:29
lhughes avatar
lhughes
The function "DNA-binding ferritin-like protein" is in Streptomyces phage Jay2Jay (BE1), but isn't on the approved list. Should we keep this in the other BE1 with the same gene call or have it removed from Jay2Jay?

Thanks,
Lee
Posted in: Functional Annotation → DNA-binding ferritin-like protein
| posted 11 Mar, 2017 03:12
lhughes avatar
lhughes
Katie:

I usually see phage on the site immediately after adding (though the information on the genes takes some time to update). I looked and don't see Warpy on the list at all.

Do you have admin rights? I'm just guessing, but that could be an issue.

Claire at WKU would be the ultimate source of information to clear up this question.

Lee
Posted in: PECAAN → Phage can not be added
| posted 19 Feb, 2017 20:55
lhughes avatar
lhughes
I am pretty sure that this is simply due to two independent autoannotations differing in some calls. If you have a class of students each run the autoannotation independently, you will find cases of this where the calls are slightly different in some cases.

Lee
Posted in: PECAAN → DNAM/PECAAN GeneMark calls differ?
| posted 03 Feb, 2017 20:41
lhughes avatar
lhughes
Thanks for the information. I'll think about what I need and determine the best solution to use.

Lee
Posted in: Phamerator → PhamDB: Make your own Phamerator databases
| posted 03 Feb, 2017 03:52
lhughes avatar
lhughes
Bump - Checking to see if anyone can answer my question about getting cluster information into a PhamDB database (see previous post).
Thanks,
Lee
Posted in: Phamerator → PhamDB: Make your own Phamerator databases
| posted 11 Jan, 2017 01:39
lhughes avatar
lhughes
Phamerator.org

You will need to set up an account (using a .edu address).

If I've misssed any details, I'm sure Steve or Vic will fill you in.

Lee
Posted in: Web Phamerator → Are we there yet?
| posted 10 Jan, 2017 04:17
lhughes avatar
lhughes
Thanks, Chris. I think we'll be fine with the Beta version for now.

Lee
Posted in: Starterator → Starterator version 1.1 released
| posted 08 Jan, 2017 02:27
lhughes avatar
lhughes
Hi Chris,

When I tried running a couple of phage on the v.1.1 version, I got an crash error after just a few phams (8 on one and 5 on the other). Both the phage I tried were BD1 phages (BeardedLady and Oliynyk). I switched back to the v.1.1.1Beta and everything seems to run fine.

Thoughts?

Lee
Posted in: Starterator → Starterator version 1.1 released