The SEED Servers
A network API for accessing the SEED data.

Archives

Categories

  • Coding Examples
    1. Some simple Sapling examples
    2. Retrieving Features and Functions for a Genome
    3. Getting a List of Genomes and Their Taxonomies
    4. Services to Support Annotation of Genes
    5. Access to Functional Coupling (Conserved Contiguity) Data
    6. Creating Custom Interfaces
    7. Metabolic Reconstructions Provided for Complete Prokaryotic Genomes
    8. Conversion of Gene and Protein IDs
  • News
    1. What SEED Do I Use?
    2. The SEED Book
    3. Upcoming Tutorials
    4. Upcoming RAST Tutorials
    5. Servers Overview
  • Technical Notes
    1. The Update Protocol for Maintenance of Annotations
  • Tutorials
    1. Some simple Sapling examples
    2. An Exercise to Get a List of Homologs of Virulence Factors
    3. An Etude Relating to a Metagenomics Sample
    4. A Short Note on Mapping PEGs to Subsystems
    5. A Short Note on Use of Server Scripts to Access Functional Coupling Scores
    6. RAST Tutorial Links
    7. Getting Summaries of Functional Content and OTUs for an Metagenomic Sample
    8. Video Tutorial: Creating a RAST Account
    9. Downloading the FIGfams
    10. Scan For Matches
    11. Getting all IDs, Aliases and Assertions of Function for One or more Protein sequences
    12. Annotating a genome using the SEED servers (via the command line or Perl code)
    13. Find Neighbors
    14. Find Gene Aliases
    15. Find Gene Function
    16. Find all features for a genome.
  • Workshop
    1. Some simple Sapling examples
    2. Accessing the Wireless Network at Argonne Tutorials and Workshops

Search

  • Master Index

API Listings

  • Sapling Server
  • Annotation Server
  • RAST Server
  • Model Server
  • Server Scripts
  • Server Utilities API

SEED Utilities

  • Scan for Matches (patscan)

About Archives

This page contains links to all the archived content.

Find recent content on the main index.

Categories

  • Coding Examples (8)
  • News (5)
  • Technical Notes (1)
  • Tutorials (16)
  • Workshop (2)

Pages

  • Introduction
  • RAST Workshop Presentation Links
  • Installation
    • Distribution of the SEED server packages
  • ModelTutorials
    • Annotations to Reactions
    • Editing Your Model
    • Generating Predictions on Your Model
    • Model Phenotypes
    • ModelView Presentation PDFs
    • Reactions to Initial Model
    • Viewing your Initial Model
  • Usage
    • 1. Summary of the Individual Servers
    • 2. Command Line Services
    • 3. The RAST batch interface

Presentations

  • Analyzing Your Genomes with the SEED Servers
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