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Nucleic Acids Research Advance Access originally published online on October 18, 2007
Nucleic Acids Research 2008 36(Database issue):D562-D571; doi:10.1093/nar/gkm758
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Nucleic Acids Research, 2008, Vol. 36, Database issue D562-D571
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

CFGP: a web-based, comparative fungal genomics platform

Jongsun Park1,2,3, Bongsoo Park1,4, Kyongyong Jung1,2, Suwang Jang1, Kwangyul Yu1, Jaeyoung Choi1,2, Sunghyung Kong1,2, Jaejin Park1,2, Seryun Kim1,2, Hyojeong Kim3, Soonok Kim3,5, Jihyun F. Kim6, Jaime E. Blair7, Kwangwon Lee8, Seogchan Kang4 and Yong-Hwan Lee1,2,3,5,*

1Fungal Bioinformatics Laboratory, 2Department of Agricultural Biotechnology, 3Center for Fungal Genetic Resource, Seoul National University, San 56-1, Sillim-9-dong, Seoul 151-921, Korea, 4Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA, 5Center for Agricultural Biomaterials, Seoul National University, San 56-1, Sillim-9-dong, Seoul 151-921, Korea, 6Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) 52 Oun-dong, Yuseong, Daejeon 305-806, Republic of Korea, 7Department of Biology, Amherst College, Amherst, MA 01002 and 8Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA

*To whom correspondence should be addressed. Tel: +82-2-880-4674; Fax: +82-2-873-2317; Email: yonglee{at}snu.ac.kr

Received July 19, 2007. Revised September 9, 2007. Accepted September 11, 2007.

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the ‘fill-in-the-form-and-press-SUBMIT’ user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.


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