FIG Tutorials

The following tutorials are available:

• Why Use the SEED (a VERY basic tutorial)?, a guide to locating relevant gene clusters.
• Getting Started, a guide to basic SEED use.
• SEED Administration, a guide to maintaining your SEED installation.
• A Simple Abstraction for Computer Scientists and Mathematicians. An attempt to bridge the cultues..
• API Tutorial, a primer on programmatic use of the SEED system.
• Data Mining, a guide to data mining with SEED.
• Phylogeny Tools, notes relating to a nascent effort to support phylogenetic analysis.
• Subsystem Tutorial, a tutorial to annotating subsystems.
• Subsystem Tutorial: a Continuation, comments on where this might lead.
• Subsystem conflict resolution
• Ambiguity and the Choice of Functional Roles
• Splitting Functional Roles

You may also find autogenerated POD documentation for the following modules:

• FIG
• P2Pupdate
• Subsystem

Random documentation and position papers:

• Project to Annotate 1000 Genomes and Produce 1000 Stoichiometric Matrices
• The Project to Annotate 1000 Genomes: An Update (Sept. 2007)
• Exchange of Assignments and Annotations
• Some Comments on Gene Functions
• Comments on a Nonstandard First Class in Bioinformatics
• The Genome Log as Implemented in the SEED: May 7, 2006
• Evidence Codes for Annotations: Initial Thoughts
• How to compare regions for a set of PEGs
• An Attempt to Make the Notion Subsystem More Precise
• Rast paper supplement: RAST to KAAS comparison
• How to Annotate a Single Genome
• Reflections on Accurate Annotations
• The Annotation Clearinghouse

Interesting Chromosomal Clusters