dictyBase--a Dictyostelium bioinformatics resource update

Abstract

dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome. This dictyBase update describes the annotations and features implemented since 2006, including improved strain and phenotype representation, integration of predicted transcriptional regulatory elements, protein domain information, biochemical pathways, improved searching and a wiki tool that allows members of the research community to provide annotations.

Figure 1.

dictyBase phenotype and strain annotations. (A) Phenotype construction using the EQ model. See text for details. (B) Strain and phenotype annotations as they appear on the dictyBase gene page. Strains are listed by a ‘strain descriptor’ on the left, with associated phenotypes to the right. The strain dhkK− appears on the dhkK gene page, while dhkK−/regA− and regA−/[act15]:dhkK(D1125N) are linked to both the dhkK and the regA genes.

Figure 2.

Regulatory elements of Dictyostelium genes. (A) Gene crlD shown in the Genome Browser window with the ‘Putative TF binding sites’ track turned on and the upstream regulatory elements displayed. Eight putative elements have been detected based on the expression profile of crlD in wild-type cells and in seven mutant cell lines. (B) Part of a report on a query for genes similar in regulatory structure and expression to the crlD gene derived from expression profiles in the comB− mutant. Sequence of the two shared motifs and gene expression in wild-type and four mutant strains are displayed.

Figure 3.

Graphical visualization of protein domains on a dictyBase gene page. The entire display is organized in the style of a ‘generic genome browser’ with the peptide on the top track and each track below representing a protein domain or domains and a source database.