Arun Aggarwal, Sam Pitluck, Frank Eeckman
Human Genome Center Informatics Group, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720
SPACE, or Sequencing Platform using ACE, is a variant of ACeDB, a suite of database, analysis, and display software originally developed by Richard Durbin and Jean Thierry-Mieg to meet the needs of the C. elegans genome research community. SPACE extends the functionality of ACeDB and builds on SynDB, an earlier LBNL variant of ACeDB used primarily for human and mouse mapping data.
Now being used in our production laboratories, SPACE's purpose is to provide additional tools to meet the evolving requirements of LBNL's sequencing and mapping projects. It differs from its predecessors primarily in the addition of a new display module which allows the simultaneous viewing of multiple, maps within the same window and in the addition of a new sequence assembly and editing tool.
For our directed sequencing effort, the assembly/editing tool is used to view pre-assembly mapping data, visually select sequence fragments, transparently set any assembly constraints, call an assembler on the selected fragments, view the results, and edit wherever necessary. Furthermore, with the flexibility of the multi-map display, different assemblies can be compared side-by-side or a given assembly can be viewed with respect to higher level mapping data. For these assemblies, we are using SPASS, a C-level routine which incorporates the Fragment Assembly Kernal (FAK) written by Gene Myers, Susan Larson, and Mudita Jain.
For our mapping efforts, the physical map display allows the viewing of loci and clones on the chromosome. And, using the multi-map, different maps, either of the same region or of different regions from different species, can be displayed. To aide in cross-species analysis, new data structures have been added to display direct homology comparisons between the species.
SPACE uses ACeDB's basic data structures, which allow all parts of the database to be easily cross-referenced, and ACeDB's user interface, which permits exploration of data via "point and click" with the computer mouse. Other ACeDB modules allow users to display and search DNA sequences for open reading frames, genes, and other features. To these core ACeDB features, LBNL has contributed a versatile query-by-example facility, a mechanism for providing on-line descriptions of data fields, and the new multi-level, multi-man display module.
*This work was supported by the U.S. Department of Energy under Contract Number DE-AC03-76SF00098
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