PomBase data update with multi-allele phenotypes

Fri, 2015-09-04

We have updated the data available on the PomBase web site to include manual curation through August 13, 2015, including 300 community-curated publications.

PomBase gene pages now include multi-allele phenotype annotations (i.e. phenotypes of double mutants, triple mutants, etc.). New sub-sections of the gene pages display multi-allele phenotypes at the population and individual cell level, paralleling the organisation of the single allele phenotype display. Compact and full views are available; both show phenotypes with the relevant genotypes and the alleles that make them up, and the full view adds details for evidence, expression, conditions, and references.

The genome browser now includes data tracks for two more publications:

DNA polymerase usage from:
Daigaku Y, Keszthelyi A, Müller CA, Miyabe I, Brooks T, Retkute R, Hubank M, Nieduszynski CA, Carr AM. 2015. A global profile of replicative polymerase usage. Nat Struct Mol Biol. 2015 Mar;22(3):192-8. doi: 10.1038/nsmb.2962 PMID:25664722

Promoters and transcription start sites from:
Li H, Hou J, Bai L, Hu C, Tong P, Kang Y, Zhao X, Shao Z. 2015. Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE. RNA Biol. 2015;12(5):525-37. doi: 10.1080/15476286.2015.1022704 PMID:25747261

Codon adaptation index (CAI) values are now included in the Protein Properties section of the gene pages and in the downloadable PeptideStats.tsv file. A file of amino acid composition data is also available from the FTP site and the Protein Datasets page.

The gene page section that was formerly misnamed "species distribution" is now called "taxonomic conservation".