Dicty WorkBench

Dictyostelium discoideum genome annotation and analysis portal

T.B.K.Reddy
San Diego Supercomputer Center
University of California, San Diego
and
The Dictyostelium Genome Project*


Click here to check human disease causing gene homologues in Dictyostelium
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This web site provides a comprehensive Dictyostelium discoideum genome annotation and analysis portal for Dicty researchers. The Dicty WorkBench is a specialized Dictyostelium sequence and function annotation database that is coupled to the Biology WorkBench. The HMMgene predicted ORFs were generated from the Dictyostelium sequencing projects* by the scientists at the respective sequencing centers and additional work by Rolf Olsen, TBK Reddy, Negin Iranfar and William Loomis at UC San Diego. The sequence BLAST runs and all other annotations were carried out at the San Diego Supercomputer Center (SDSC). The Dicty database is an Oracle object-relational database with the query interface, Seeker, developed by Roger Unwin. The framework for the database was abstracted from the Biology WorkBench development and from the Alliance for Cellular Signaling(AFCS) Projects lead by Dr.Shankar Subramaniam. The funding support for the above two projects came from the National Institutes of Health (NIH) and the National Science Foundation (NSF). Annotated Dictyostelium proteome is presented here in the form of a searchable and sortable database.

You may Browse the entire list of predicted ORFs listed by ORFID and Protein Name. By clicking on any column heading in a table you can sort the results. Either you can enter the Annotation Table from the browsed list by clicking on an interested ORF or you can straight go to search Dicty annotation table for a protein of your interest by protein name or ORFID or Contig number etc. Links are provided to ORF Details BLAST and PFAM domain analysis results. These links will help in the easy navigation between different tables. By clicking on any word in a row you can search using same word as a search term. Otherwise you may compose your own search criteria with multiple and/or options on any table. Links are provided to import sequences to Biology WorkBench for further analysis. In Summary the following features are available for querying.

Both nucleotide and protein sequences of all HMM predicted ORFs (from sanger and Jena contigs) and selected 8,000 plus sequences are now integrated as blastable databases into Biology WorkBench. The Biology WorkBench is a revolutionary web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. You may conduct your own analyses on any selected ORF at Biology WorkBench by importing either nucleic acid or amino acid sequences. You will find links to import an ORF sequences in ORF Details, Annotation and PFAM Results tables. Dicty annotation pages coupled with Biology WorkBench will serve as valuable and versatile resources for Dicty researchers.

Questions Comments and Suggestions regarding this portal may be addressed to reddy@sdsc.edu

*The Dictyostelium Genome Project : The Baylor Sequencing Center, Houston, Texas, (A. Kuspa and R. Gibbs) where sequencing is supported by the NIH; the Institute of Biochemistry, Cologne together with the Institute of Molecular Biotechnology, Jena, Germany (G. Glöckner , A. Rosenthal, L. Eichinger and A. Noegel) where sequencing is supported by the Deutsche Forschungsgemeinschaft (No 113/10-1 and 10-2).; and the EUDICT consortium supported by The European Union (M-A. Rajandream, D. Lawson and B. Barrell). Guidelines on use of data in publications are available at http://www.sanger.ac.uk/Projects/use-policy.shtml and http://www.uni-koeln.de/dictyostelium/guidelines.shtml.