Abstract
BackgroundThe SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups.ResultsThe currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java.ConclusionsWe present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.
Highlights
The (The database and infrastructure for comparative genomics) (SEED) integrates many publicly available genome sequences into a single resource
The SEED currently contains over 850 Bacterial genomes that have been completely sequenced (Table 1; The SEED contains many hundreds of draft genomes.) For several years it has been realized that the most efficient and accurate way of annotating these genomes is not by considering each in isolation, but by comparing them all together in unified integration platforms [1]
The SEED platform provides the underpinnings to several common microbial genome annotation services (Fig.1)
Summary
The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The SEED http://www.theseed.org/ contains all publicly available genome sequences. The Rapid Annotation using Subsystem Technology (RAST server) provides high throughput accurate annotations for complete microbial genomes [6,7]. The development of the RAST server for complete microbial genome annotation provides consistent and accurate annotations, automatic connections to metabolic reconstructions, and detailed comparative genomics tools pre-
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