- One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012. [PMID: 23494302]
Petra Fey, Robert J Dodson, Siddhartha Basu, Rex L Chisholm
Methods in molecular biology (Clifton, N.J.) 2013:983
18 Citations (Google Scholar as of 2016-01-26)
Abstract: dictyBase (http://dictybase.org), the model organism database for Dictyostelium discoideum, includes the complete genome sequence and expression data for this organism. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. dictyBase has recently expanded to include the genome sequences of three additional Dictyostelids and has added new software tools to facilitate multigenome comparisons. The Dicty Stock Center, a strain and plasmid repository for Dictyostelium research, has relocated to Northwestern University in 2009. This allowed us integrating all Dictyostelium resources to better serve the research community. In this chapter, we will describe how to navigate the Web site and highlight some of our newer improvements.
- DictyBase 2013: integrating multiple Dictyostelid species. [PMID: 23172289]
Siddhartha Basu, Petra Fey, Yogesh Pandit, Robert Dodson, Warren A Kibbe, Rex L Chisholm
Nucleic acids research 2013:41(Database issue)
27 Citations (Google Scholar as of 2016-01-26)
Abstract: dictyBase (http://dictybase.org) is the model organism database for the social amoeba Dictyostelium discoideum. This contribution provides an update on dictyBase that has been previously presented. During the past 3 years, dictyBase has taken significant strides toward becoming a genome portal for the whole Amoebozoa clade. In its latest release, dictyBase has scaled up to host multiple Dictyostelids, including Dictyostelium purpureum [Sucgang, Kuo, Tian, Salerno, Parikh, Feasley, Dalin, Tu, Huang, Barry et al.(2011) (Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol., 12, R20)], Dictyostelium fasciculatum and Polysphondylium pallidum [Heidel, Lawal, Felder, Schilde, Helps, Tunggal, Rivero, John, Schleicher, Eichinger et al. (2011) (Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res., 21, 1882-1891)]. The new release includes a new Genome Browser with RNAseq expression, interspecies Basic Local Alignment Search Tool alignments and a unified Basic Local Alignment Search Tool search for cross-species comparisons.
- dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. [PMID: 21087999]
Pascale Gaudet, Petra Fey, Siddhartha Basu, Yulia A Bushmanova, Robert Dodson, Kerry A Sheppard, Eric M Just, Warren A Kibbe, Rex L Chisholm
Nucleic acids research 2011:39(Database issue)
29 Citations (Google Scholar as of 2016-01-26)
Abstract: dictyBase (http://www.dictybase.org), the model organism database for Dictyostelium, aims to provide the broad biomedical research community with well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase 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 to provide a 'reference genome' in the Amoebozoa clade. We highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase.
- dictyBase--a Dictyostelium bioinformatics resource update. [PMID: 18974179]
Petra Fey, Pascale Gaudet, Tomaz Curk, Blaz Zupan, Eric M Just, Siddhartha Basu, Sohel N Merchant, Yulia A Bushmanova, Gad Shaulsky, Warren A Kibbe, Rex L Chisholm
Nucleic acids research 2009:37(Database issue)
54 Citations (Google Scholar as of 2016-01-26)
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.