Bioinformatics Advance Access originally published online on January 28, 2005
Bioinformatics 2005 21(5):696-697; doi:10.1093/bioinformatics/bti250
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DictyMOLD-a Dictyostelium discoideum genome browser database
1 IMB Jena, Department of Genome Analysis Beutenbergstrasse 11, 07745 Jena, Germany
2 Center for Biochemistry, Medical Faculty, University of Cologne Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany
*To whom correspondence should be addressed.
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Abstract |
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 TOP Abstract INTRODUCTIONTHE DictyMOLD INTERFACEREFERENCES |
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Summary: With the Dictyostelium Genome Project nearing completion, we initiated the construction of a data repository for all Dictyostelium discoideum genomic data. Up to now this database, called DictyMOLD (Dicty Map Of Linked Data), incorporates the recently completed D.discoideum chromosomes 1 and 2 sequences together with related annotations. To visualise maps, sequences and annotations and to provide access for the scientific community a perl-based browser was developed.
Availability: The DictyMOLD database is freely accessible via http://genome.imb-jena.de/dictyostelium/
Contact: gernot{at}imb-jena.de
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INTRODUCTION |
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TOPAbstractINTRODUCTIONTHE DictyMOLD INTERFACEREFERENCES |
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The lower eukaryote Dictyostelium discoideum is a well suited model for the investigation of cell functions related to growth, motility, differentiation and development (Loomis, 1996). An international effort to sequence the genome of this organism was initiated in 1998 (Kay and Williams, 1999). The current version of the sequence assembly (May 2002 freeze) covers
6.8 Mb of chromosome 2 (C2) in 66 ordered and oriented contigs (Glöckner et al., 2002). Another 0.9 Mb of C2 sequence is available but not mapped yet. The chromosome 1 (C1) assembly (July 2003 freeze) covers with 4.7 Mb the whole unique part of the chromosome in 4 ordered and oriented contigs (G. Glöckner, unpublished data). Using the gene prediction program GeneID (Parra et al., 2000)in the gene prediction process for C1 and C2 yielded, in total, 4599 predicted genes >40 amino acids (C1: 1770 genes; C2: 2829 genes). BLAST searches (Altschul et al., 1990) were used to determine the chromosomal location of D.discoideum repetitive elements (Glöckner et al., 2001), mapping markers (Williams and Firtel, 2000) and ESTs (Morio et al., 1998).
The amino acid sequences of all predicted genes were compared to the full sets of proteins from completed model organism genomes as well as against SWISS-PROT and TrEMBL. They were also checked for the presence of InterPro domains using the InterPro database (Apweiler et al., 2000). The gene ontology terminology (http://www.geneontology.org/) (The Gene Ontology Consortium, 2000) was applied to determine potential roles for the proteins in the cell.
To facilitate storage and exploration of the data, we developed the DictyMOLD genome browser together with its underlying database.
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THE DictyMOLD INTERFACE |
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To enter the chromosome browser different possibilities are offered. Two of the entry points can be accessed via http://genome.imb-jena.de/cgi-bin/dicty/analysis.cgi. From there further links lead to a search interface and the genome browser. The search page provides an easy way to query the DictyMOLD database with search strings (e.g. gene identifiers, InterPro numbers). The users can also enter the chromosome browser via a second link, through a specially developed DictyMOLD interface. The web interface allows easy access to selected regions by clicking on the appropriate sequence range of the chromosomes that are schematically represented on this page. Alternatively the search function can be used to search for gene identifiers, accession numbers, HAPPY markers, ESTs and direct access to the corresponding chromosomal location is provided.
The user can navigate through the chromosome and zoom between a 100 kb (Fig. 1) and a 10 kb range view using navigation buttons. The graphical representation of each annotated gene incorporates a direct link to the data sheet containing all available information about the gene product. The third entry point to the DictyMOLD database is provided via a BLAST Server.
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The current version of DictyMOLD provides a basic set of annotations that will be expanded in the future. Furthermore, the database will soon be extended to chromosome 3.
Additional D.discoideum databases are available under: http://dictybase.org, http://dictygenome.bcm.tmc.edu/, http://www.sanger.ac.uk/Projects/D_discoideum/, http://www.uni-koeln.de/dictyostelium/ and http://glamdring.ucsd.edu/others/dsmith/dictydb.html.
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Acknowledgments |
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We thank the members of the Japanese cDNA project and The Dictyostelium Genome Sequencing Consortium for sharing their data. The D.discoideum genome project is funded by the Deutsche Forschungsgemeinschaft (DFG), the National Institutes of Health (NIH), the Medical Research Council (MRC) and the European Union (EU). M.F. was supported by the Deutsche Forschungsgemeinschaft (grant PL173/5–2).
Received on January 14, 2004; revised on February 23, 2004; accepted on January 5, 2005
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REFERENCES |
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