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

@article{citeulike:3106917, 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.}, address = {Korean BioInformation Center, KRIBB, Daejeon 305-806 and Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea. bulee@kribb.re.kr}, author = {Lee, B. and Lee, D.}, citeulike-article-id = {3106917}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/18411203}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=18411203}, day = {1}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {domain-architecture, protein-sequence-similarity}, month = {July}, number = {Web Server issue}, posted-at = {2008-08-11 00:18:46}, priority = {2}, title = {DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/18411203}, volume = {36}, year = {2008} }

TY - JOUR ID - citeulike:3106917 L3 - citeulike-article-id:3106917 N2 - 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. IS - Web Server issue JF - Nucleic acids research SN - 1362-4962 AD - Korean BioInformation Center, KRIBB, Daejeon 305-806 and Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea. bulee@kribb.re.kr TI - DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture. VL - 36 KW - domain-architecture KW - protein-sequence-similarity AU - Lee, B AU - Lee, D PY - 2008/07/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/18411203 ER -