Genomic database resources for Dictyostelium discoideum

Dictyostelium is an attractive model system for the study of mechanisms basic to cellular function or complex multicellular developmental processes. Recent advances in Dictyostelium genomics have generated a wide spectrum of resources. However, much of the current genomic sequence information is still not currently available through GenBank or related databases. Thus, many investigators are unaware that extensive sequence data from Dictyostelium has been compiled, or of its availability and access. Here, we discuss progress in Dictyostelium genomics and gene annotation, and highlight the primary portals for sequence access, manipulation and analysis (http://genome.imb-jena.de/dictyostelium/; http://dictygenome.bcm.tmc.edu/; http://www.sanger. ac.uk/Projects/D_discoideum/; http://www.csm.biol. tsukuba.ac.jp/cDNAproject.html).

[1]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[2]  A. Kuspa,et al.  Ordered yeast artificial chromosome clones representing the Dictyostelium discoideum genome. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[3]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[4]  A. Kuspa,et al.  Tagging developmental genes in Dictyostelium by restriction enzyme-mediated integration of plasmid DNA. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Y. Suzuki,et al.  Construction of full-length-enriched cDNA libraries. The oligo-capping method. , 2001, Methods in molecular biology.

[6]  A. Kimmel,et al.  CHAPTER 7 – The Organization and Expression of the Dictyostelium Genome , 1982 .

[7]  A. Kimmel,et al.  Sequence organization in Dictyostelium: unique structure at the 5'-ends of protein coding genes. , 1983, Nucleic acids research.

[8]  Peter R. Cook,et al.  Happy mapping: linkage mapping using a physical analogue of meiosis , 1993, Nucleic Acids Res..

[9]  W. Loomis.  The Development of Dictyostelium Discoideum , 1982 .

[10]  M. Quail,et al.  The complex repeats of Dictyostelium discoideum. , 2001, Genome research.

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

[12]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[13]  Victor V. Solovyev,et al.  The Gene-Finder Computer Tools for Analysis of Human and Model Organisms Genome Sequences , 1997, ISMB.

[14]  S. Salzberg,et al.  Interpolated Markov models for eukaryotic gene finding. , 1999, Genomics.

[15]  P. Dear,et al.  A high-resolution HAPPY map of Dictyostelium discoideum chromosome 6. , 2000, Genome research.

[16]  T. Saito,et al.  The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.