CFGP 2.0: A versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes

Jaeyoung Choi, Kyeongchae Cheong, Kyongyong Jung, Jongbum Jeon, Gir Won Lee, Seogchan Kang, Sangsoo Kim, Yin Won Lee, Yong Hwan Lee

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

In 2007, Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr/ ) was publicly open with 65 genomes corresponding to 58 fungal and Oomycete species. The CFGP provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since 2007, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants and 105 animals. In addition, the number of tools in Favorite increased to 27. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, several systematic platforms designed to support studies on selected gene families have been developed. Most of them are connected through Favorite to allow of sharing data across the platforms.

Original languageEnglish (US)
JournalNucleic acids research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013

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Oomycetes
Genomics
Fungi
Genome
Information Dissemination
Information Storage and Retrieval
Computational Biology
Genes
Bacteria

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Choi, Jaeyoung ; Cheong, Kyeongchae ; Jung, Kyongyong ; Jeon, Jongbum ; Lee, Gir Won ; Kang, Seogchan ; Kim, Sangsoo ; Lee, Yin Won ; Lee, Yong Hwan. / CFGP 2.0 : A versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. In: Nucleic acids research. 2013 ; Vol. 41, No. D1.
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CFGP 2.0 : A versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. / Choi, Jaeyoung; Cheong, Kyeongchae; Jung, Kyongyong; Jeon, Jongbum; Lee, Gir Won; Kang, Seogchan; Kim, Sangsoo; Lee, Yin Won; Lee, Yong Hwan.

In: Nucleic acids research, Vol. 41, No. D1, 01.01.2013.

Research output: Contribution to journalArticle

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