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

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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 c 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.krandhttp://localodom.kobic.re.kr/dahunter/index.htm.
Publisher
OXFORD UNIV PRESS
Issue Date
2008-07
Language
English
Article Type
Article
Keywords

SEQUENCE; INFORMATION; EVOLUTION; FAMILIES; RESOURCE; DATABASE; UNIVERSE

Citation

NUCLEIC ACIDS RESEARCH, v.36, pp.W60 - W64

ISSN
0305-1048
DOI
10.1093/nar/gkn172
URI
http://hdl.handle.net/10203/18466
Appears in Collection
BiS-Journal Papers(저널논문)
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