Homologues identification: This is the first step in homology the homologues will be unknown. We have many protein databases such as PROSITE, where we modeling. We have to get the homologues to the sequence we have. There will be several number of homologues to the given equation. But most of can go with a sequence alignment so that we can get the homologues for the sequence we have. Since we have a very large sequence that is genome, the protein sequence will be large too. We can identify homologues with the sequence or with the protein based on its structure.