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Recent Activity

Debbie Jacobs-Sera posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

Debbie Jacobs-Sera posted in Capsid maturation protease and MuF-like fusion protein

Debbie Jacobs-Sera posted in frame shift

New HHPred web site

Link to this post \| posted 24 May, 2017 18:43
delesall	Has anybody tried to use the new HHPred web site? I'm curious about which database we should select to run query?

Link to this post \| posted 26 May, 2017 02:13
jparker	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? Jordan

Link to this post \| posted 30 May, 2017 15:14
cdshaffer	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.

Link to this post \| posted 30 May, 2017 15:23
delesall	Hi Chris What databases do you pick to run a search? The menu of databases is much smaller, right?

Link to this post \| posted 30 May, 2017 21:42
cdshaffer	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.

Link to this post \| posted 30 May, 2017 22:45
delesall	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) http://scop.berkeley.edu

Link to this post \| posted 21 Jul, 2017 12:56
kklyczek	I just noticed that several databases have been added, and the current choices include: PDB SCOPe95 SCOPe70 COG_KOG Pfam-A NCBI_conserved_domains SMART TIGRFAM PRK 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

Link to this post \| posted 09 Aug, 2017 15:17
welkin	Hi All, I think we have decided that the best choices for now are: PDB pFam CDD SCOPe 70 The link to the new HHPred website is here, in case anyone has trouble finding it: https://toolkit.tuebingen.mpg.de/#/tools/hhpred However, as of 11am Eastern, on 8.8.2017, the site says it is undergoing maintenance. Hopefully it will be up again shortly! Best, Welkin

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

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