论文信息 - dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa

dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa

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.

[1] David L. Steffen,et al. The genome of the social amoeba Dictyostelium discoideum , 2005, Nature.

[2] Hideko Urushihara,et al. The cDNA sequencing project. , 2006, Methods in molecular biology.

[3] S. Lewis,et al. The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[4] Rafael C. Jimenez,et al. The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[5] C. Stoeckert,et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[6] R. Yoshino,et al. The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization , 2000, Molecular and General Genetics MGG.

[7] Adam Kuspa,et al. Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. , 2003, Nucleic acids research.

[8] Thomas Winckler,et al. Molecular Phylogeny and Evolution of Morphology in the Social Amoebas , 2006, Science.

[9] Blaz Zupan,et al. dictyBase—a Dictyostelium bioinformatics resource update , 2008, Nucleic Acids Res..

[10] Eric M. Just,et al. dictyBase, the model organism database for Dictyostelium discoideum , 2005, Nucleic Acids Res..

[11] Erik L. L. Sonnhammer,et al. InParanoid 6: eukaryotic ortholog clusters with inparalogs , 2007, Nucleic Acids Res..