high-throughput domain discovery

Question

[blur]

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,

Answer 1

[Selenocysteine]

Hmmer + Pfam

http://hmmer.org/

http://pfam.xfam.org/

Answer 2

[Joe]

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.

Answer 3

[martinsteinegger]

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.