<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>

Did you consider [PFAM][1] database?

**'Domain Organizations'** are very beautifully prepared. Look at [this][2]

You can search what domains are present in a protein sequence with `hmmscan` tool, searching the sequence against a [HMM][3] database of PFAM

 [1]: http://pfam.xfam.org/
 [2]: http://pfam.xfam.org/family/pf00406#tabview=tab1
 [3]: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release