Annotated list of Getting Started, Tutorial and Coding Examples

Getting Started	Links
A page of links exploring the recent RAST tutorials	RAST Tutorial Links
An introduction to the Fellowship for the Interpretation of Genomes, creators of the SEED	What is FIG
How to get a RAST account and access it to set your password	Video Tutorial: Creating a RAST Account
How to download, install and try out the SEED servers client code	Accessing the SEED Servers: Getting Started

Using the "svr" command line scripts	Links
Using svr command line scripts to retrieve all the features for a given genome. This is often the first step in an analysis sequence.	Find all features for a genome.
Using the svr command-line scripts to download all the genes for a genome.	Downloading a Genome
Using svr command-line scripts to get the roles and features of a subsystem.	Downloading a Subsystem
Using the svr command-line scripts to access the complete set of FIGfams.	Downloading the FIGfams
Using the svr command line scripts to access the Annotation Clearinghouse.  How to see all of the assignments made by any group to a protein having the same sequence.	Getting all IDs, Aliases and Assertions of Function for One or more Protein sequences
Using svr command line scripts to find PEGs that are in the neighborhood of a given PEG.	Find Neighbors
Using svr command line scripts to see all the aliases by which a given feature or set of features is known in the SEED.	Find Gene Aliases
Using svr command line scripts to retrieve the assigned function for each of a set of genes.	Find Gene Function
Using svr command line scripts to retrieve all the features for a given genome. This is often the first step in an analysis sequence.	Find all features for a genome.
Two methods of doing annotations with the SEED servers   1. How to use svr command line scripts to do genome annotation: call the RNA-encoding genes and protein-encoding genes, asserts  functions for the gene products, and produces an initial metabolic reconstruction.   2.  How to use the Server Perl API to call the RNAs, PEGs, identify the functions, and generate an initial metabolic reconstruction.	Annotating a genome using the SEED servers (via the command line or Perl code)

Using the Server Perl API	Links
Using the Server Perl API to: 1.   Identify Genes 2.   Assign Functions to Encoded Proteins 3.   Create a Metabolic Reconstruction	Services to Support Annotation of Genes
Discussion of the example (Example 4) that uses the SEED servers Perl API  to access to the data used to compute co-occurrence scores.	Access to Functional Coupling (Conserved Contiguity) Data
Discussion of server Perl API Example 3 illustrating the functions required to determine the location of a SEED gene encoding a specific protein and to acquire the genes from a given region centered on that location.	Creating Custom Interfaces
Using the server Perl API to identify the subsystems can be inferred from a  set of functional roles.	Metabolic Reconstructions Provided for Complete Prokaryotic Genomes
Using the server Perl API to illustrate basic capabilities that relate to determining the set of IDs attached to specific protein sequences.	Conversion of Gene and Protein IDs

Metagenomics	Links
Using the RAST servers for Metagenomics	Getting Summaries of Functional Content and OTUs for an Metagenomic Sample