TABLE OF CONTENTS


INTRODUCTION

I.  A TOUR THROUGH BIRCH
     I.1  Hierarchical directory structure
     I.2  Managing a sequencing project
     I.3  General analysis: FSAP
     I.4  Databases
          I.4.1  Description of databases
          I.4.2  Searching for and retrieving data from databases
          I.4.3  Database subset management: XYLEM
     I.5  Phylogeny construction
     I.6  Network resources

II.  GETTING STARTED
     II.1  What is an operating system, and why do we need to know
          how to use it?
     II.2  What you need to learn
          II.2.1  The core commands
          II.2.2  The vi text editor
          II.2.3  File organization
     II.3  Connecting to the system
          II.3.1  Ethernet connection
          II.3.2  Connecting to UMNET by modem or wire
          II.3.3  Campus network resources
     II.4  Setting up your account

III.  HOW TO DO THINGS
     III.1  General guidelines
          III.1.1  Environment variables: shorthand ways of specifying
               directories
          III.1.2  How to find a program
          III.1.3  Finding and printing documentation
          III.1.5  File formats
          III.1.4  Executing program
          III.1.6  Citing programs and data in publications
     III.2  Finding and retrieving sequences
          III.2.1  Retrieving sequences by name or accession number
          III.2.2  Keyword searches
          III.2.3  What if fetch can't find your sequence?
          III.2.4  Creating your own database subsets
     III.3  Searching databases.
          III.3.1  General guidelines for database searching
          III.3.2  Automated searches of GenBank: search and dsearch 
          III.3.3  Direct use of fasta, tfasta and ssearch lets you
               customize your search parameters
          III.3.4   Evaluating the significance of sequence
                    similarities
     III.4  Extracting and Manipulating Sequence Features
          III.4.1  The DDBJ/EMBL/GenBank FEATURES Language
          III.4.2  features: a menu-driven user-interface to getob
          III.4.3  Extracting a Feature from a GenBank Entry
          III.4.4  Extracting One or More Features from Groups of
               Entries
          III.4.5  Extracting Features Using Expressions
          III.4.6  Creating Your Own Sequences: Feature Expressions
     III.5  Other database tasks
          III.5.1  Submitting a nucleic acid sequence for inclusion in
               GenBank
          III.5.2  Reporting database errors to GenBank
     III.6  Networks: navigating the Internet
          III.6.1  Electronic mail
          III.6.2  Electronic bulletin boards (Newsgroups)
          III.6.3  Running remote terminal sessions: telnet
          III.6.4  Remote file transfer: FTP
          III.6.5 Network resource applications

IV.  APPENDICIES
     Appendix A - Programs Listed by Function.
     Appendix B - Database files
     Appendix C - Sequence File Formats
     Appendix D - The DDBJ/EMBL/GenBank Features Table
     Appendix E - Literature Citations for Programs

INDEX.