Comments (7)
Thank you @croth1 for such a quick response!
from hh-suite.
Hi @merkys, thanks for spotting this. We recently switched to a new webserver. The new link is:
http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsearch_dbs/
from hh-suite.
I believe this is broken again.
from hh-suite.
Hi altaetran
For hhsearch you can use the same databases as hhblits uses at:
http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
HHpred is currently unsupported. We are currently reworking it and making it able to use mmCIF structures, but this is not ready for prime time yet.
The old unsupported databases are still available here:
http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/
from hh-suite.
Has there been any update on the HHpred front? Or is it still unsupported?
Any links to download the databases from?
from hh-suite.
Nothing new to report yet. Sorry!
from hh-suite.
Just to make sure I have the correct understanding of this:
- HHsuite has a bunch of programs -- hhblits: does sequence alignment -- against databases provided to it.
- HHpred can use the result of those alignments (or do them itself, given other programs are present) and through the use of modeller make predictions of protein structures.
It is the 2nd part (HHpred) that is causing trouble with missing A3M databases -- so a wok around this would be that we use (for now while you fix this) the results from HHblits -- get possible templates - and then then manually work with those templates to produce alignments and then use Modeller to get protein structures. Does this summarise it? Or is there some essential point that I missed.
from hh-suite.
Related Issues (20)
- issue using cstranslate
- ERROR building database for HHsuite using cstranslate
- HMM-HMM comparison - beginner
- Does the template searching result contain query sequence's structure or not?
- Does the template searching result contain query sequence's structure or not? HOT 3
- HHsearch - inconsistent results HOT 1
- HHblits failed
- hhmake issue
- hhmake issue
- c++: fatal error: Killed signal terminated program cc1plus HOT 1
- error while loading shared libraries: libHH_OBJECTS.so HOT 2
- Request to update the PDB70 database HOT 3
- Both HHBlits and HHSearch give misaligned indels for homologous sequences
- PackagesNotFoundError HOT 3
- HHblits Prefiltering database run time on Supercomputer Cluster HOT 3
- Segmentation fault with ffindex_apply -- hhmake
- Python 3.11 Support HOT 1
- 您好 制作属于自己的蛋白质数据集时出了问题
- Using hh-suites to find E.coli gene in other Proteobacteria <advice on the way I am using the method>
- Pfam36 Update HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hh-suite.