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Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W60-4. doi: 10.1093/nar/gkn172. Epub 2008 Apr 14.

DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture.

Author information

1
Korean BioInformation Center, KRIBB, Daejeon 305-806 and Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea. bulee@kribb.re.kr

Abstract

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 gamma 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.

PMID:
18411203
PMCID:
PMC2447808
DOI:
10.1093/nar/gkn172
[Indexed for MEDLINE]
Free PMC Article

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