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

New HHPred web site

| posted 24 May, 2017 18:43
Has anybody tried to use the new HHPred web site? I'm curious about which database we should select to run query?
| posted 26 May, 2017 02:13
I have tried, but the new HHPred site refuses to work for me. Connection errors, freezing, just refusing to have anything happen which I click buttons. Has anyone gotten it to work?
| posted 30 May, 2017 15:14
The new site is working for me. Just in case it is a browser issue: I used the chrome browser on a mac in the past and I just tried chrome on my windows 7 virtual machine worked ok there as well.
| posted 30 May, 2017 15:23
Hi Chris

What databases do you pick to run a search? The menu of databases is much smaller, right?
| posted 30 May, 2017 21:42
When I am doing de novo annotation and I like to maximize sensitivity and on the old system that meant I would pick most of the databases. With the new site I am only getting 4 listed. I have been going with the default PDB because I was just double checking. I would probably add the Scope95 and the Pfam when I want a broad search with maximum sensitivity.
| posted 30 May, 2017 22:45
OK - I only see 4 databases as well. We have been selecting PDB and Pfam but not Scope. Since these are do novo annotation, I may add Scope95. However, the Scope database may disappear this summer per information on their web site (assuming I'm not confusing web sites)
| posted 21 Jul, 2017 12:56
I just noticed that several databases have been added, and the current choices include:

I think the annotation guide in the past has recommended using PDG, Pfam, and TIGRFAM. I am not familiar with some of the others but will do some exploring.
Edited 21 Jul, 2017 12:56
| posted 09 Aug, 2017 15:17
Hi All,
I think we have decided that the best choices for now are:
SCOPe 70

The link to the new HHPred website is here, in case anyone has trouble finding it:

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

| posted 07 Nov, 2017 04:54
Hey PHriends!
Does anyone have a set of guides as to the colours of matches in the HHPred results?


Login to post a reply.