What is the best tool I can use to search for protein domains ?

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Alexander Koval

CDD – Conserved Domain Database

http://www.ncbi.nlm.nih.gov

in the Resources menu select "Domains & Structures"

"Conserved Domain Database (CDD)".

Meriem Fassatoui

Thanks Alexander for your help. What about Hiden Markov Model ?

You are welcome. Sorry, my answer is late.

Here is the tool for Hidden Markov Model studying.

http://pfam.xfam.org

Enter your protein of interest ID or fragment of protein sequence, search.

Then click from the left colomn the option "HMM logo". Voila.

For example: http://pfam.xfam.org/family/PF02285#tabview=tab4

HMM logo for mitochondrial cytochrome oxidase subunit 8.