The Genome Sequence DataBase: towards an integrated functional genomics resource

Skupski, M. P., Booker, M., Farmer, A., Harpold, M., Huang, W., Inman, J., Kiphart, D., Kodira, C., Root, S., Schilkey, F., Schwertfeger, J., Siepel, A., Stamper, D., Thayer, N., Thompson, R., Wortman, J., Zhuang, J. J., Harger, C. (1999) The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Research, 27 (1). pp. 35-8. ISSN 0305-1048

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URL: http://www.ncbi.nlm.nih.gov/pubmed/9847136
DOI: 10.1093/nar/27.1.35

Abstract

During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.

Item Type: Paper
Uncontrolled Keywords: Animals *Base Sequence Computational Biology Consensus Sequence *Databases, Factual Gene Expression *Genome Genome, Human Humans *Information Storage and Retrieval Sequence Alignment
Subjects: bioinformatics > genomics and proteomics > databases
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 12 Jan 2015 21:52
Last Modified: 12 Jan 2015 21:52
PMCID: PMC148091
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31108

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