SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models

• Published in: PloS one Vol. 7; no. 10; p. e48053
• Main Authors: Aziz, Ramy K, Devoid, Scott, Disz, Terrence, Edwards, Robert A, Henry, Christopher S, Olsen, Gary J, Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Stevens, Rick L, Vonstein, Veronika, Xia, Fangfang
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 24-10-2012; Public Library of Science (PLoS)
• Subjects: Acids; Analysis; Annotations; BASIC (programming language); Biological computing; Biological effects; Biology; Biotechnology; Collection; Computational Biology - methods; Computer applications; Computer Science; Controlled vocabularies; Data bases; Data processing; Databases, Factual - statistics & numerical data; Escherichia coli - genetics; Escherichia coli - metabolism; Gene sequencing; Genomes; Genomics; Genomics - methods; Genomics - statistics & numerical data; Information Storage and Retrieval - methods; Internet; Laboratories; Leprosy; Mathematics; Metabolic flux; Metabolism; Metabolomics - methods; Metabolomics - statistics & numerical data; Microbiology; Microorganisms; Molecular Sequence Annotation - methods; Molecular Sequence Annotation - statistics & numerical data; Ontology; Protein families; Relational data bases; Reproducibility of Results; Servers; Servers (computers); Software; Chicago Illinois; California; United States > US; Illinois
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0048053

The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users.