CFGP: a web-based, comparative fungal genomics platform

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.

Characterization of PIR1, a GATA family transcription factor involved in iron responses in the white-rot fungus Phanerochaete chrysosporium

“…The same conclusion can be reached from the vast majority of the SRE sequences depicted in the Supplementary Fig. S2 (employing the Comparative Fungal Genomics Platform (CFGP); Park et al, 2008). Those from N. crassa, B. dermatitidis, Histoplasma capsulatum and A. nidulans possess two small introns interrupting the zinc finger domains (Gauthier et al, 2010).…”

Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

“…The development of algorithms that can find conserved or known motifs in promoter sequences has been instrumental, particularly when combined with global TF-binding data (Hu et al 2010;Reid et al 2010). Phylogenetic footprinting (Cliften et al 2003;Kellis et al 2003;Borneman et al 2007;Tuch et al 2008;Lavoie et al 2010) and nucleosome location data (Narlikar et al 2007;Gordan et al 2009) can enhance the probability that conserved motifs represent functional UASs (Wingender et al 1996;Monteiro et al 2008;Park et al 2008). Genomewide mapping of 59 mRNA ends (Miura et al 2006;Nagalakshmi et al 2008) and newly discovered or revised binding site preferences for .100 yeast transcription factors have also improved the ability to associate conserved motifs with known or suspected TFs.…”

The ER Chaperone LHS1 Is Involved in Asexual Development and Rice Infection by the Blast FungusMagnaporthe oryzae

“…We searched for putative Hsp70 homologs in the M. oryzae genome using the InterProScan program incorporated in a bioinformatics portal system, Comparative Fungal Genomics Platform (Park et al, 2008) (Table 1). Thirteen proteins were identified to contain Hsp70-related domains (IPR001023, Hsp70; IPR013126, Hsp70; IPR012725, Chaperone DnaK; note that IPR001023 is the secondary accession number of IPR013126) (see Supplemental Figure 1 online).…”