CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

• Published in: Bioinformatics Vol. 20; no. 18; pp. 3682 - 3686
• Main Authors: Hallin, Peter F., Ussery, David W.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 12.12.2004; Oxford Publishing Limited (England)
• Subjects: Algorithms; Biological and medical sciences; Computational Biology - methods; Database Management Systems; Databases, Nucleic Acid; Deoxyribonucleic acid; DNA; Fundamental and applied biological sciences. Psychology; General aspects; Information Dissemination - methods; Information Storage and Retrieval - methods; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Sequence Alignment - methods; Sequence Analysis, DNA - methods; User-Computer Interface; Database; Storage; Genome; Bioinformatics
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bth423

Currently, new bacterial genomes are being published on a monthly basis. With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis. More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists. In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics. DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page. Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues. Availability: A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/ Supplementary information: This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase