<p>Hi,</p>

<p>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.</p>

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.