Question: high-throughput domain discovery
1
gravatar for blur
18 months ago by
blur110
European Union
blur110 wrote:

Hi, I want to take a very large list of proteins and check to see if they harbor any interesting domains. Is there a tool or a DB I can download to work with?

Thanks,

proteins domain • 414 views
ADD COMMENTlink modified 3 months ago by martinsteinegger20 • written 18 months ago by blur110
0
gravatar for Selenocysteine
18 months ago by
Dublin, Ireland
Selenocysteine550 wrote:

Hmmer + Pfam

http://hmmer.org/

http://pfam.xfam.org/

ADD COMMENTlink modified 18 months ago • written 18 months ago by Selenocysteine550
0
gravatar for jrj.healey
18 months ago by
jrj.healey13k
United Kingdom
jrj.healey13k wrote:

HHsuite https://github.com/soedinglab/hh-suite

The databases and software can be downloaded and run locally. I regularly do several hundred proteins through my local install with some additional scripts to agregate the results.

ADD COMMENTlink written 18 months ago by jrj.healey13k
0
gravatar for martinsteinegger
3 months ago by
martinsteinegger20 wrote:

I am biased since I am the developers of MMseqs2. MMseqs2 can perform fast sequence/profile searches. It is possible to annotate 1.1 billion protein sequences with Pfam domains in 8.3 h on a 2×14-core server. Here is a guide how to setup the search.

ADD COMMENTlink modified 3 months ago • written 3 months ago by martinsteinegger20
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