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. 2007 Jan 9:8:9.
doi: 10.1186/1471-2164-8-9.

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists

Alexandre Gattiker  1 , Riccarda Rischatsch, Philippe Demougin, Sylvia Voegeli, Fred S Dietrich, Peter Philippsen, Michael Primig
Affiliations

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists

Alexandre Gattiker et al. BMC Genomics. .

Abstract

Background: The Ashbya Genome Database (AGD) 3.0 is an innovative cross-species genome and transcriptome browser based on release 40 of the Ensembl developer environment.

Description: AGD 3.0 provides information on 4726 protein-encoding loci and 293 non-coding RNA genes present in the genome of the filamentous fungus Ashbya gossypii. A synteny viewer depicts the chromosomal location and orientation of orthologous genes in the budding yeast Saccharomyces cerevisiae. Genome-wide expression profiling data obtained with high-density oligonucleotide microarrays (GeneChips) are available for nearly all currently annotated protein-coding loci in A. gossypii and S. cerevisiae.

Conclusion: AGD 3.0 hence provides yeast- and genome biologists with comprehensive report pages including reliable DNA annotation, Gene Ontology terms associated with S. cerevisiae orthologues and RNA expression data as well as numerous links to external sources of information. The database is accessible at http://agd.vital-it.ch/.

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Figures

Figure 1
Figure 1
The synteny viewer. Panel a displays syntenic chromosomal regions from A. gossypii and S. cerevisiae. Panel b shows different levels of the MultiContigView as indicated where homologous genes in a given region are connected with lines.
Figure 2
Figure 2
Microarray expression data for A. gossypii and S. cerevisiae. Panel a gives an overview of the genomic localization of genes. The target sequences recognized by microarray oligonucleotide probes present on the Ashbya GeneChip (SYNG001a) are indicated in green. Panels b and c show a bar diagram of normalized array expression signals obtained with germinating Ashbya spores and hyphae growing on rich medium compared to data obtained for the budding yeast orthologs expressed on various growth and sporulation media as indicated.
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