Introduction to Sequence Analysis using EMBOSS

Tutorial based on the command line execution of bioinformatics programs.

 

CONTENTS

• What is EMBOSS?
  • So, what is EMBOSS?
  • Working with EMBOSS
  • wossname: a first EMBOSS application
    • Exercise: wossname
• Working with sequences
  • Retrieving sequences from databases
    • Exercise: showdb
    • seqret
    • Exercise: seqret
• Pairwise sequence alignment
  • Dotplots
    • Exercise: Making a dotplot
  • Global alignment
    • Exercise: needle
  • Local alignment
    • Exercise: water
• Protein analysis
  • Identifying the ORF
    • Exercise: plotorf
    • Exercise: getorf
  • Translating the sequence
    • Exercise: transeq
  • Secondary structure prediction
    • pepinfo
    • Exercise: pepinfo
    • Predicting transmembrane regions
    • Exercise: tmap
• Patterns, profiles and multiple sequence alignment
  • Pattern matching
    • Exercise: patmatmotifs
  • Protein fingerprints
    • Exercise: pscan
  • Multiple Sequence Analysis
    • Exercise: Retrieving a set of sequences
    • Exercise: emma
    • Exercise: prettyplot
  • Profiles
    • Exercise: prophecy
    • Exercise: prophet
• Conclusion