ArticleNucleic acids research2008
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Placental DNA Methylation Abnormalities in Prenatal Conotruncal Heart Defects.Frontiers in genetics · 2022Article
- Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree.Proteins · 2017Article
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins.Bioinformation · 2013Article
- Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors.Genes · 2011Article
- FACT: functional annotation transfer between proteins with similar feature architectures.BMC bioinformatics · 2010Article
- Protein comparison at the domain architecture level.BMC bioinformatics · 2009Article
- d-Omix: a mixer of generic protein domain analysis tools.Nucleic acids research · 2009Article
- ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes.Nucleic acids research · 2009Article
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2 authors.
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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.
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