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The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes

C Harger¹, M Skupski, E Allen

¹National Center for Genome Resources, 1800A Old Pecos Trail, Santa Fe, NM 87505, USA. cah@ncgr.org

Nucleic Acids Research

|January 1, 1997

Summary

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The Genome Sequence DataBase (GSDB) now offers GSDB 1.0, a new relational database for genomic data. This enhanced platform supports new data types and improved access for researchers.

Area of Science:

Bioinformatics
Genomics
Database Management

Background:

The Genome Sequence DataBase (GSDB) previously utilized a less efficient database structure.
Managing and accessing diverse genomic data types presented challenges.

Purpose of the Study:

To upgrade the GSDB to a robust relational database system.
To enhance data contribution and retrieval mechanisms for genomic sequences and annotations.

Main Methods:

Conversion to an improved relational database architecture (GSDB 1.0).
Implementation of a graphical client-server interface tool (GSDB Annotator) for data submission.
Development of GIO (GSDB Input/Output) files for data exchange.
Introduction of a new Web Query Tool and direct SQL access for data retrieval.

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Main Results:

GSDB 1.0 is fully operational and publicly accessible.
New data types, including discontiguous sequences, multiple sequence alignments, and community annotations, are now supported.
Streamlined data contribution and retrieval processes are established.

Conclusions:

The upgraded GSDB 1.0 provides a more efficient and comprehensive platform for genomic data management.
Enhanced accessibility and support for diverse data formats will facilitate genomic research and collaboration.