Nucleic Acids Research Advance Access published online on April 14, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn172
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DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture
1Korean BioInformation Center, KRIBB, Daejeon 305-806 and 2Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea
*To whom correspondence should be addressed. Tel: +82 42 879 8531; Fax: +82 42 879 8519; Email: bulee{at}kribb.re.kr Correspondence may also be addressed to Doheon Lee. Tel: +82 42 869 4316; Fax: +82 42 869 8680; Email: dhlee{at}biosoft.kaist.ac.kr
Received February 9, 2008. Revised March 17, 2008. Accepted March 25, 2008.
We present DAhunter, a web-based server that identifies homologous proteins by comparing domain architectures, the organization of protein domains. A major obstacle in comparison of domain architecture is the existence of ‘promiscuous’ domains, which carry out auxiliary functions and appear in many unrelated proteins. To distinguish these promiscuous domains from protein domains, we assigned a weight score to each domain extracted from RefSeq proteins, based on its abundance and versatility. A domain's score represents its importance in the ‘protein world’ and is used in the comparison of domain architectures. In scoring domains, DAhunter also considers domain combinations as well as single domains. To measure the similarity of two domain architectures, we developed several methods that are based on algorithms used in information retrieval (the cosine similarity, the Goodman–Kruskal 
function, and domain duplication index) and then combined these into a similarity score. Compared with other domain architecture algorithms, DAhunter is better at identifying homology. The server is available at http://www.dahunter.kr and http://localodom.kobic.re.kr/dahunter/index.htm
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