accessingthe s e e d servers getting started（accessingthe s e e d服务器开始）.docVIP

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accessingthe s e e d servers getting started（accessingthe s e e d服务器开始）.doc

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* Table of Contents Introduction 8 The SEED Project 8 What is FIG? 8 The FIG Architecture: the SEED 9 Components of the SEED Annotation System 11 The SEED, the A-SEED, the P-SEED, and the PubSEED 11 SEED 11 Annotators SEED (A-SEED) 11 PATRIC SEED (P-SEED) 11 Public SEED (PubSEED) 11 What SEED Do I Use? 11 Ownership of Genomes 12 Setting Up an Annotation Group 15 Access of Data Via the Servers 15 Maintenance of Subsystems 16 Subsystems 17 FIGfams 17 RAST 18 Metabolic Modeling 19 Model Tutorials 19 Metagenomics 20 Annotating your Genome 21 Basic Steps in Annotating a Prokaryotic Genome 21 Running Your Genome Through RAST 21 Walking Your Genome 21 Building a Metabolic Reconstruction 22 Summary 23 Annotating a Genome Using RAST 23 Running Your Genome Through RAST 24 Walking your Genome Using RAST 24 Exporting Your Genome from RAST 29 Annotating a Genome with myRAST 29 Running a Genome Through myRAST 30 Walking your Genome Using myRAST 32 Exporting Your Genome from myRAST 33 Metabolic Modeling 35 Modeling Overview 35 Accessing The SEED Database 37 The Entity-Relationship Model 37 Summary of Individual Servers 38 The Sapling Server 38 The Annotation Support Server 38 The RAST server 38 The Model Server 39 Getting Started 39 Getting started with Command Line svr scripts 39 Getting started writing Perl scripts to access the servers 41 Using the Command Line Scripts 43 A (Very) Minimal Introduction to Some Basic Command-Line Tools 43 Command Line Services 47 Find all features for a genome. 48 Find Gene Function 48 Find Gene Aliases 49 Find Neighbors 50 More Examples 51 The RAST Batch Interface 51 Advanced Programming with the Servers 54 Getting a list of Genomes and Their Taxonomies 54 Listing All Genomes 54 Taxonomy 55 Retrieving Features and Functions for a Genome 56 Conversion of Gene and Protein ID’s 58 Example 1 Discussion 59 Output Table 60 Metabolic Reconstructions Provided for Complete Prokaryotic Genomes 60 Example 2 Discussion 60 Example 2 Input File (Truncated) 6