1. Summary of the Individual Servers

The Sapling Server (API)

The SAPserver.pm package offers programmatic access to the data maintained in the Sapling DB within the SEED.  The Sapling DB is described by an entity-relationship model that depicts the basic entities maintained within the database and the relationships that we have encoded between them.  This offers the basic foundation upon which most of the SEED toolkit resides. The methods offered by Sapling Objects support a rich set of operations against genomic data.  Using the methods described in the API, the user has access to genomes, annotations, functional coupling data, protein families, subsystems, and a rapidly growing number of more specialized forms of data. 

 To see the overall ER diagram and the relations that implement it see the Sapling webpage.

A complete tutorial is offered in SAP tutorial.

The Annotation Support Server (API)

The ANNOserver.pm package supports capabilities relating to annotation of genomes.  It supports invocation of standard gene callers (Glimmer3 for protein-encoding genes), and newly-developed high-performace methods to assign function to protein sequences or regions of DNA fragments (based on FIGfams and a unique use of K-mers that act as signatures of FIGfams).  We include an example application based on these methods that can be used to produce relatively acurate annotation of most microbial genomes within a few minutes.

The RAST server (API)

RAST is a publicly-available server for the annotation of microbial genomes.  It is maintained by a team at Argonne National Lab and FIG.  Currently, it has over 2600 registered users, and several thousand genomes have been run through the service in the last couple of years (often several times!).  The RASTserver.pm package was created to support programmatic submision of genomes to RAST, the retrieval of status, and the retrieval of the final set of annotations.  

The Model Server (API)

This server provides access to all data associated with the biochemistry database and the genome-scale metabolic models stored within the SEED. This server also provides the user with the ability to run a set of simple flux balance analysis studies with the SEED models. A detailed description of the interface is here.