Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Syndb: A Multi-Species Database For Mapping and Sequence Information

A. Aggarwal, D. Davy, J. McCarthy, E. Theil
Human Genome Informatics Group, Lawrence Berkeley Laboratory, Berkeley, CA 94720

Syndb is a variant of ACeDB, a suite of database and display software originally developed by Richard Durbin and Jean Thierry-Mieg to meet the needs of the C. elegans genome research community. Syndb extends the functionality of ACeDB and builds on 21Bdb, another LBL variant of ACEDB used to maintain a public version of LBL's Chromosome 21 Project data.

Currently under active development, Syndb's purpose is to provide additional tools to meet the evolving requirements of LBL's mapping and sequencing projects. It differs from its predecessors primarily in the addition of a new display module which allows the simultaneous viewing of multiple maps of different species from within the same database or of different levels of physical detail of a single map. Also, new data structures have been added to display direct homology comparison in the multiple species display.

Syndb 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, LBL has contributed a versatile query-by-example facility, a mechanism for providing on-line descriptions of data fields, and the new multi-level, multimap display module. Comments and suggestions on all aspects of these new map display capabilities, from the underlying data structures to the visual appearance of the interface are earnestly solicited.

Syndb has replaced 21Bdb as the primary mechanism for providing data from LBL's physical mapping and sequencing projects to other researchers throughout the world. Like 21Bdb, remote access to the full Unix version of Syndb will be available to anyone on the Internet running X-windows software, or via anonymous FTP for remote installation, and as part of the World Wide Web (WWW) via "front-end" ACEDB gateway software developed by Guy Decoux at INRA in France.

Since 1992, LBL has been a major contributor to the ongoing development of ACeDB and related tools, along with its original authors, and a growing user community. Support for this fruitful collaboration comes from the Department of Energy's Human Genome Project; the U.C. Berkeley Drosophila Mapping Project sponsored by NIH; and the U.S. Department of Agriculture's Plant Genome Database Project at the National Agricultural Library. External data sources include Genbank, the Genome Data Base (GDB), the International Genome Database (IGD), Genethon, CEPH, and Jackson Laboratory's Encyclopedia of the Mouse.