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, 43 (Database issue), D656-61

PomBase 2015: Updates to the Fission Yeast Database

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PomBase 2015: Updates to the Fission Yeast Database

Mark D McDowall et al. Nucleic Acids Res.

Abstract

PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecular and phenotypic annotations, through to the display of genome-wide high-throughput studies. Recent improvements to the site extend annotation specificity, improve usability and allow for monthly data updates. Both in-house curators and community researchers provide manually curated data to PomBase. The genome browser provides access to published high-throughput data sets and the genomes of three additional Schizosaccharomyces species (Schizosaccharomyces cryophilus, Schizosaccharomyces japonicus and Schizosaccharomyces octosporus).

Figures

Figure 1.
Figure 1.
Views available in the genome browser. (A) Region display with two tracks enabled, displaying RNA-Seq coverage data (12). The two tracks show the forward (top) and reverse (bottom) strand reads along with the genes that are mapped to the region. (B) Region comparison display showing the regions of alignment between Schizosaccharomyces pombe and Schizosaccharomyces japonicus (top) and Schizosaccharomyces octosporus (bottom) in green. (C) Gene tree view generated using the Compara framework, with the gene of interest, pom1 (SPAC2F7.03c), highlighted in red.
Figure 2.
Figure 2.
PomBase gene page views for example annotations: (A) GO (gene ste11 - SPBC32C12.02); (B) FYPO (gene cdc2 - SPBC11B10.09); (C) Gene expression (gene clr3 - SPBC800.03). These examples highlight the display of annotation extensions and their use within the context of different ontologies.

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