protein domain software

Question

[elmira b]

Hi,

Would you please recommend me a good software for searching domains in a protein or coding nucleotide sequence? (except NCBI conserved domain search). Your help is greatly appreciated.

Answer 1

[venu]

Did you consider PFAM database?

'Domain Organizations' are very beautifully prepared. Look at this

You can search what domains are present in a protein sequence with hmmscan tool, searching the sequence against a HMM database of PFAM

[elmira b]

Thank you so much!

Answer 2

[Antonio R. Franco]

My favorites for proteins are

• InterPro (where you can find domains and get lots of information using InterProScan). You can also use InterProScan with nucleic acids
  • The UniProt database

Answer 3

[shelly.deforte]

I decided to use Prosite for a project I'm working on because it has the best integration with UniProt. One of the problems with Pfam is that it is not updated nearly as often as UniProt is, and so your domain intervals are sometimes out of synch. Prosite is updated with UniProt, and you can pull the Prosite domains directly from UniProt, i.e.

http://www.uniprot.org/uniprot/?sort=score&desc=&query=id:Q12851&format=tab&columns=id,feature(DOMAIN%20EXTENT)

While I'm not aware of any out of the box packages for searching domains, you can write a custom script to pull the domain information you need fairly easily.

[venu]

Convinced with the Update point. The last update of Pfam was in 2013. Found a tool in similarity search box here. Spending some time on this can be useful to find the domain in the target sequence in an easy way.

Answer 4

[verma]

Hey Hi Elmira,

Please try to use The Consurf Server (http://consurf.tau.ac.il/). It may work to sort out your problem.

Regards,
Garima Verma

Answer 5

[Elisabeth Gasteiger]

Have you tried the ScanProsite tool, http://prosite.expasy.org/scanprosite? Unfortunately there are currently some issues with this tool and the server is not fully functional, but you could check back in a few days.

You could also try to download the command line tool behind ScanProsite and use it to scan your local copy of UniProtKB against your own patterns or against PROSITE signatures:

ftp://ftp.expasy.org/databases/prosite/ps_scan/