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

About this Entry

This page contains a single entry by The SEED Team published on September 2, 2010 12:05 PM.

RAST Tutorial Links was the previous entry in this blog.

A Short Note on Use of Server Scripts to Access Functional Coupling Scores is the next entry in this blog.

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