The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at

All posts created by welkin

| posted 24 Apr, 2018 12:18
Posted in: Request a new function on the SEA-PHAGES official listDprA DNA processing chain A
| posted 20 Apr, 2018 12:25
Try this work-around from our IT person:

"So as I mentioned, the problem was that as a regular user - windows had an issue with the software being from an "untrusted" developer.

I used the Application Compatibility Toolkit to manually add the title to the windows whitelist for such things. After that, no problem running as a regular user.

I used this guide to resolve the problem, substituting the windows 8.1 versions where appropriate:​

Edited 24 Apr, 2018 12:18
Posted in: DNA MasterRunning with Administrator Privileges
| posted 19 Apr, 2018 14:51
Yes, looks like Squiddly has two integrases, including one of the same ones that appears in several other gordonias with two integrases: Howe, Utz, Bowser.

And yes, you can have two tyrosine ones. We talk about it in the Gordonia paper:

Good catch!
Posted in: Cluster DN Annotation TipsMultiple Integrases?
| posted 18 Apr, 2018 15:58
I think we should be conservative here and not call anything. I have seen some BLAST results between Bs and other clusters, but the gene organization is not conserved: that is, the genes in Bs with BLAST hits don't have a downstream ORF with a substantial overlap in a different frame. There is something else going on in these phages.
Posted in: Cluster B Annotation TipsTail assembly chaperones?
| posted 18 Apr, 2018 15:55
We do not know where the capsid maturation protease or scaffolding proteins are for Cluster D.
Posted in: Cluster D Annotation Tipsprotease and scaffolding
| posted 18 Apr, 2018 15:55
we do not know where the frameshift is in Cluster D.
Posted in: Cluster D Annotation TipsTail assembly chaperones?
| posted 18 Apr, 2018 14:36
Lee Hughes
Welkin Pope
Crosby is for Sidney, no?

Wasn't sure what you were asking until I googled it smile
I just can't even…. You are sentenced to watch play-off hockey for at least another week.
Posted in: Request a new function on the SEA-PHAGES official listDNA binding protein, HU-like
| posted 17 Apr, 2018 18:49
sounds good to me. make it HU-like domain though. Crosby is for Sidney, no?
Edited 17 Apr, 2018 18:51
Posted in: Request a new function on the SEA-PHAGES official listDNA binding protein, HU-like
| posted 17 Apr, 2018 18:48
I think there are several issues here.
some misguided phage biologists call the portal protein a "head to tail connector". The portal is not a head to tail connector.
There are other smaller proteins that make a complex that binds to the portal and bottom of the capsid in the "neck" region; and these proteins we call the "head-to-tail connector complex" proteins. There are several different ones and we are using a catch-all term for now to address them.

However, in some of the crystal structure papers, the portal has been crystallized with several of the head-to-tail connector complex proteins in a big complex. When you align a true httcc protein with HHPred to the PDB, you may retrieve these records, which may include a portal. This can be confusing, because it looks like your result is a portal. it isn't.

1) if you already have a portal upstream of the terminase, that's your portal. you don't have another one.
2) you have to have a crystal structure alignment with HHPred to use the term "head-to-tail connector complex". We have changed our criteria for this assignment in the past year, so the database is currently riddled with genes that do not meet this criteria, and need to be corrected. BLAST on phagesdb is not enough, because we know there are things in there that are not correct and need to be fixed.
Posted in: Functional AnnotationHead-tail connectors
| posted 17 Apr, 2018 12:56
Cluster AR contains a phage that was not isolated and sequenced by the SEA-PHAGES program. Its finders annotated the genome differently. We do not curate, update, or QC this genome.

This phage is:

Edited 22 Oct, 2019 14:04
Posted in: Cluster AR Annotation Tipsnon SEA-PHAGES genomes