Contents

• Basics
  • Resources
    • Electronic Resources
    • Textbooks
    • Journal sources
  • UNIX Operating Systems
    • Logging on/off
    • UNIX File System
    • Commands
    • Help
    • Redirection
    • Shells
    • Special `hidden' files
    • Background Processes
    • Utilities
    • Scripts-Languages
    • Editors
    • Communications
    • Mail
  • Letter Codes for Sequences
• Databases
  • Introduction
  • N.C.B.I.
  • E.M.B.L.
  • D.D.B.J.
  • SwissProt
  • Organization of the entries
  • Other Major Databases
  • Remote Database Entry retrieval
    • Entrez
    • NCBI retrieve
    • EMBL get
    • Others
  • Reliability
• Database Searching
  • Are there homologues in the database?
    • FASTA
      • Instructions
      • FASTA output
      • FASTA format
      • Statistical Significance
    • BLAST
      • BLAST output
      • BLAST format
    • BLITZ
      • BLITZ output
      • BLITZ format
  • BLOCKS
    • BLOCKS output
    • BLOCKS format
    • Getting the Block
  • SSearch
  • Why you should routinely check your sequence
• Internet
  • A few internet facts
  • USENET
  • BIONET
  • telnet
  • ftp
  • Web Search Engines
  • Useful Sites
  • List Servers
  • File Servers
  • EMBL Software Server
    • Baylor College of Medicine
  • Finding an Address
  • Finding Software - Archie
    • Veronica
  • WAIS
  • WWW
  • Database of Databases: LiMB
• Sequence Alignment
  • Dot Plots
    • The Exact Way
    • Identity Blocks
  • Alignments
    • The Needleman and Wunsch Algorithm
    • The Smith-Waterman Algorithm
  • Testing Significance
  • Gaps and Indels
    • ``Natural" Gap Weights - Thorne, Kishino & Felsenstein
  • Multiple Sequence Alignments
• Distance Measures
  • Nucleotide Distance Measures
    • Simple counts as a distance measure
    • Jukes - Cantor Correction
    • Kimura 2-parameter Correction
    • Tamura - Nei Correction
    • Uneven spatial distribution of substitutions
    • Synonymous - nonsynonymous substitutions
  • Amino acid distance measures
    • PAM Matrices
    • BLOSUM Matrices
    • GONNET Matrix
  • Gap Weighting
• Reconstructing Phylogenies
  • Introduction
    • Purpose
    • Trees of what
    • Terminology
    • Controversy
  • Distance Methods
  • Parsimony Methods
  • Other Methods
    • Compatibility methods
    • Maximum Likelihood methods
    • Method of Invariants
    • Quartet Methods
  • Warnings
  • Available Packages
  • PHYLIP
    • PHYLIP Contents
• Pattern Analysis
  • Information Theory
    • Patchiness
  • Chargaff's Rules
  • Sequence Conservation
    • E. coli Promoters
    • Analysis of Sequence Motifs
    • Information Content of Sequence Motifs
    • Searching for Sequence Motifs
• Exon Analysis
  • Open Reading Frames
    • Gene Recognition
    • Software
    • Summary
  • Codon Usage
    • Codon Pattern by Position
    • Synonymous Codon Choices and Codon Bias
    • Synonymous Codon Bias and the Divergence Rate of Genes