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

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Title
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture
Author(s)
ByungUk Lee; D Lee
Bibliographic Citation
Nucleic Acids Research, vol. 36, no. Sup 2, pp. W60-W64
Publication Year
2008
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.
ISSN
0305-1048
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/nar/gkn172
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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