CFGP: A web-based, comparative fungal genomics platform

Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Jaeyoung Choi, Sunghyung Kong, Jaejin Park, Seryun Kim, Hyojeong Kim, Soonok Kim, Jihyun F. Kim, Jaime E. Blair, Kwangwon Lee, Seogchan Kang, Yong Hwan Lee

Research output: Contribution to journalArticle

67 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)D562-D571
JournalNucleic acids research
Volume36
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 1 2008

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Genomics
Genome
Informatics
Computational Biology
Saccharomyces cerevisiae
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Park, J., Park, B., Jung, K., Jang, S., Yu, K., Choi, J., ... Lee, Y. H. (2008). CFGP: A web-based, comparative fungal genomics platform. Nucleic acids research, 36(SUPPL. 1), D562-D571. https://doi.org/10.1093/nar/gkm758
Park, Jongsun ; Park, Bongsoo ; Jung, Kyongyong ; Jang, Suwang ; Yu, Kwangyul ; Choi, Jaeyoung ; Kong, Sunghyung ; Park, Jaejin ; Kim, Seryun ; Kim, Hyojeong ; Kim, Soonok ; Kim, Jihyun F. ; Blair, Jaime E. ; Lee, Kwangwon ; Kang, Seogchan ; Lee, Yong Hwan. / CFGP : A web-based, comparative fungal genomics platform. In: Nucleic acids research. 2008 ; Vol. 36, No. SUPPL. 1. pp. D562-D571.
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Park, J, Park, B, Jung, K, Jang, S, Yu, K, Choi, J, Kong, S, Park, J, Kim, S, Kim, H, Kim, S, Kim, JF, Blair, JE, Lee, K, Kang, S & Lee, YH 2008, 'CFGP: A web-based, comparative fungal genomics platform', Nucleic acids research, vol. 36, no. SUPPL. 1, pp. D562-D571. https://doi.org/10.1093/nar/gkm758

CFGP : A web-based, comparative fungal genomics platform. / Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F.; Blair, Jaime E.; Lee, Kwangwon; Kang, Seogchan; Lee, Yong Hwan.

In: Nucleic acids research, Vol. 36, No. SUPPL. 1, 01.01.2008, p. D562-D571.

Research output: Contribution to journalArticle

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Park J, Park B, Jung K, Jang S, Yu K, Choi J et al. CFGP: A web-based, comparative fungal genomics platform. Nucleic acids research. 2008 Jan 1;36(SUPPL. 1):D562-D571. https://doi.org/10.1093/nar/gkm758