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CFGP: a web-based, comparative fungal genomics platform.

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 - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, San 56-1, Sillim-9-dong, Seoul 151-921, Korea.

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.

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Structure of DUI. (A) A screenshot shows the process of data acquisition from Contig Browser. On the left side, ‘Data Frame’ displays the list of Magnaporthe oryzae proteins and ‘Manipulation Frame’ on the right side shows a list of Favorite. The ‘Collection arrow’ in the middle transfers chosen sequences from the Data Frame to the Manipulation Frame. (B) Collected sequences can be analysed by data analysis tools in Favorite. Users can choose sequences by clicking the checkbox in front of each sequence. (C) A BLAST search output is shown with Favorite in the Manipulation Frame. From the BLAST result, users can transfer sequences to Favorite via the use of the ‘Collection Arrow’.
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Figure 2: Structure of DUI. (A) A screenshot shows the process of data acquisition from Contig Browser. On the left side, ‘Data Frame’ displays the list of Magnaporthe oryzae proteins and ‘Manipulation Frame’ on the right side shows a list of Favorite. The ‘Collection arrow’ in the middle transfers chosen sequences from the Data Frame to the Manipulation Frame. (B) Collected sequences can be analysed by data analysis tools in Favorite. Users can choose sequences by clicking the checkbox in front of each sequence. (C) A BLAST search output is shown with Favorite in the Manipulation Frame. From the BLAST result, users can transfer sequences to Favorite via the use of the ‘Collection Arrow’.

Mentions: We developed the DUI to seamlessly support data management and integrative analyses using a suite of data analysis tools. It consists of two compartments: the Data Frame, supports browsing and collection of data, and the Manipulation Frame, which supports data management (Figure 2A). Four browsing tools under the ‘SEQUENCE’ menu include Contig Browser for browsing data in the data warehouse, SequenceSet Browser for browsing data in databases such as Uniprot, MyGene Browser for browsing data in the user's own computer and NR Browser for NR and NT sequences of NCBI. The Manipulation Frame provides a mechanism for storing and organizing data collected in a personalized space in the CFGP. The collection arrow transfers selected sequence data from the Data Frame to the Manipulation Frame, where they can be analysed by any bioinfomatic tools in the CFGP. This data management scheme significantly enhances the efficiency of data analysis, especially when large amounts of data are involved.Figure 2.


CFGP: a web-based, comparative fungal genomics platform.

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 - Nucleic Acids Res. (2007)

Structure of DUI. (A) A screenshot shows the process of data acquisition from Contig Browser. On the left side, ‘Data Frame’ displays the list of Magnaporthe oryzae proteins and ‘Manipulation Frame’ on the right side shows a list of Favorite. The ‘Collection arrow’ in the middle transfers chosen sequences from the Data Frame to the Manipulation Frame. (B) Collected sequences can be analysed by data analysis tools in Favorite. Users can choose sequences by clicking the checkbox in front of each sequence. (C) A BLAST search output is shown with Favorite in the Manipulation Frame. From the BLAST result, users can transfer sequences to Favorite via the use of the ‘Collection Arrow’.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238957&req=5

Figure 2: Structure of DUI. (A) A screenshot shows the process of data acquisition from Contig Browser. On the left side, ‘Data Frame’ displays the list of Magnaporthe oryzae proteins and ‘Manipulation Frame’ on the right side shows a list of Favorite. The ‘Collection arrow’ in the middle transfers chosen sequences from the Data Frame to the Manipulation Frame. (B) Collected sequences can be analysed by data analysis tools in Favorite. Users can choose sequences by clicking the checkbox in front of each sequence. (C) A BLAST search output is shown with Favorite in the Manipulation Frame. From the BLAST result, users can transfer sequences to Favorite via the use of the ‘Collection Arrow’.
Mentions: We developed the DUI to seamlessly support data management and integrative analyses using a suite of data analysis tools. It consists of two compartments: the Data Frame, supports browsing and collection of data, and the Manipulation Frame, which supports data management (Figure 2A). Four browsing tools under the ‘SEQUENCE’ menu include Contig Browser for browsing data in the data warehouse, SequenceSet Browser for browsing data in databases such as Uniprot, MyGene Browser for browsing data in the user's own computer and NR Browser for NR and NT sequences of NCBI. The Manipulation Frame provides a mechanism for storing and organizing data collected in a personalized space in the CFGP. The collection arrow transfers selected sequence data from the Data Frame to the Manipulation Frame, where they can be analysed by any bioinfomatic tools in the CFGP. This data management scheme significantly enhances the efficiency of data analysis, especially when large amounts of data are involved.Figure 2.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, San 56-1, Sillim-9-dong, Seoul 151-921, Korea.

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.

Show MeSH