This is a test version of Biostars. For the public version, visit https://www.biostars.org.
high-throughput domain discovery

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,

domain proteins
• 2,251 views • link
updated by martinsteinegger • martinsteinegger • written by blur blur

3 answers

Hmmer + Pfam

http://hmmer.org/

http://pfam.xfam.org/

• 0 views • link
written by Selenocysteine Selenocysteine

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.

• 0 views • link
written by Joe Joe

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.

• 0 views • link
written by martinsteinegger • martinsteinegger

Log in to answer this question.

More posts like this