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PHI-base update: additions to the pathogen host interaction database.

Winnenburg R, Urban M, Beacham A, Baldwin TK, Holland S, Lindeberg M, Hansen H, Rawlings C, Hammond-Kosack KE, Köhler J - Nucleic Acids Res. (2007)

Bottom Line: The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts.In parallel, the curation process has been improved and now involves several external experts.On the technical side, several new search tools have been provided and the database is also now distributed in XML format.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomathematics and Bioinformatics, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, AL5 2JQ, UK.

ABSTRACT
The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/.

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Related in: MedlinePlus

Predicted virulence genes for the newly sequenced fish pathogen V. salmonicida (Vs). Vs genes are displayed as circles, PHI-base genes are displayed as rectangles and are colour coded to indicate type. The arcs between the genes represent sequence–homology relationships. The visualization tool has placed ∼50 putative Vs virulence genes in V. salmonicida into distinct clusters of PHI-base entries.
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Figure 1: Predicted virulence genes for the newly sequenced fish pathogen V. salmonicida (Vs). Vs genes are displayed as circles, PHI-base genes are displayed as rectangles and are colour coded to indicate type. The arcs between the genes represent sequence–homology relationships. The visualization tool has placed ∼50 putative Vs virulence genes in V. salmonicida into distinct clusters of PHI-base entries.

Mentions: The most common application of PHI-base is to use the database for the identification of pathogenicity genes arising either from comparative genomics analyses (3) or from forward genetics analyses in a different organism (2). However, the PHI-base data is also increasingly being used to annotate newly sequenced genomes and EST projects. For example, using the ONDEX system (8), the genome of the fish pathogen Vibrio salmonicida was annotated effectively (Figure 1). To identify putative virulence factors in this newly sequenced organism, the following steps were done within the data integration system ONDEX: (i) XML format of PHI-base uploaded; (ii) homologues identified using an e-value of <10−6; (iii) BLAST hits further filtered so that only genes which aligned across more than 50% of their length remained and (iv) the results were loaded into the graph analysis component of the ONDEX system (Figure 1). This analysis identified 50 putative virulence factors in V. salmonicida.Figure 1.


PHI-base update: additions to the pathogen host interaction database.

Winnenburg R, Urban M, Beacham A, Baldwin TK, Holland S, Lindeberg M, Hansen H, Rawlings C, Hammond-Kosack KE, Köhler J - Nucleic Acids Res. (2007)

Predicted virulence genes for the newly sequenced fish pathogen V. salmonicida (Vs). Vs genes are displayed as circles, PHI-base genes are displayed as rectangles and are colour coded to indicate type. The arcs between the genes represent sequence–homology relationships. The visualization tool has placed ∼50 putative Vs virulence genes in V. salmonicida into distinct clusters of PHI-base entries.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238852&req=5

Figure 1: Predicted virulence genes for the newly sequenced fish pathogen V. salmonicida (Vs). Vs genes are displayed as circles, PHI-base genes are displayed as rectangles and are colour coded to indicate type. The arcs between the genes represent sequence–homology relationships. The visualization tool has placed ∼50 putative Vs virulence genes in V. salmonicida into distinct clusters of PHI-base entries.
Mentions: The most common application of PHI-base is to use the database for the identification of pathogenicity genes arising either from comparative genomics analyses (3) or from forward genetics analyses in a different organism (2). However, the PHI-base data is also increasingly being used to annotate newly sequenced genomes and EST projects. For example, using the ONDEX system (8), the genome of the fish pathogen Vibrio salmonicida was annotated effectively (Figure 1). To identify putative virulence factors in this newly sequenced organism, the following steps were done within the data integration system ONDEX: (i) XML format of PHI-base uploaded; (ii) homologues identified using an e-value of <10−6; (iii) BLAST hits further filtered so that only genes which aligned across more than 50% of their length remained and (iv) the results were loaded into the graph analysis component of the ONDEX system (Figure 1). This analysis identified 50 putative virulence factors in V. salmonicida.Figure 1.

Bottom Line: The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts.In parallel, the curation process has been improved and now involves several external experts.On the technical side, several new search tools have been provided and the database is also now distributed in XML format.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomathematics and Bioinformatics, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, AL5 2JQ, UK.

ABSTRACT
The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/.

Show MeSH
Related in: MedlinePlus