<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>

My favorites for proteins are

 - [InterPro][1] (where you can find domains and get lots of information using InterProScan). You can also use InterProScan with nucleic acids
- The [UniProt database][2]

 [1]: http://www.ebi.ac.uk/interpro/
 [2]: http://www.uniprot.org/