7 research outputs found
Additional file 2: of Modeling central metabolism and energy biosynthesis across microbial life
Supplemental data table associated with this study. There are twelve data tabs included in this table. Description for each data tab is at the end of “Additional file 1” document. (XLSX 2418 kb
Additional file 1: of Modeling central metabolism and energy biosynthesis across microbial life
Supplemental figures and figure descriptions. In addition, descriptions for each supplemental data tabs in “Additional file 2” are included at the end of the document. (DOCX 17183 kb
16S alignment file
Sequence alignment file that has been used to generate the initial master tree. Based on this master tree, the microbial life tree that was used in this study (16S OTU98.5) was generated using a distance-based clustering algorithm
Microbial life tree (16S OTU98.5)
Phylogenetic tree (nwk format) used to show pathway conservation analysis on central metabolis
SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models
<div><p>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 (<a href="http://www.theseed.org/servers">http://www.theseed.org/servers</a>): 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.</p> </div
Architecture of the SEED servers.
<p>The client packages (currently available for Perl or Java) handle the HTTP requests and responses, and parse the data from the appropriate lightweight data exchange formats to data structures. The four servers access the SEED data.</p
Processing ids_to_sequences.
<p>(a) The ids_to_sequences function call accepts multiple IDs as an argument and uses the Sapling server to process the calls. These are returned as a single table. (b) A detailed description of each call (in this example, the ids_to_sequences) is provided online and is automatically generated from the entity-relationship models shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048053#pone-0048053-g002" target="_blank">Figure 2</a>.</p