Table of Contents

4.1. How this Tutorial is Organised

4.1.1. wossname: a first EMBOSS Application

4.1.2. Exercise: wossname

4.2. Working with Sequences

4.2.1. Retrieving Sequences from Databases

4.2.2. Exercise: showdb

4.2.3. seqret

4.2.4. Exercise: seqret

4.2.5. Reading Sequences from Files

4.2.6. infoseq

4.2.7. Sequence Annotation

4.2.8. Using Multiple Sequences

4.2.9. Listfiles

4.3. Working with Alignments

4.3.1. Pairwise Sequence Alignment

4.3.2. Dotplots

4.3.3. Exercise: Making a Dotplot

4.3.4. Exercise: Examining Dotplot Parameters

4.3.5. Global Alignment

4.3.6. Exercise: needle

4.3.7. Local Alignment

4.3.8. Exercise: water

4.4. Protein Analysis

4.4.1. Identifying the ORF

4.4.2. Exercise: plotorf

4.4.3. Exercise: getorf

4.4.4. Translating the Sequence

4.4.5. Exercise: transeq

4.4.6. USA for Partial Sequences

4.5. Secondary Structure Prediction

4.5.1. pepinfo

4.5.2. Exercise: pepinfo

4.5.3. Predicting Transmembrane Regions

4.5.4. Exercise: tmap

4.6. Patterns, Profiles and Multiple Sequence Alignment

4.6.1. Pattern Matching

4.6.2. Exercise: patmatmotifs

4.6.3. Protein Fingerprints

4.6.4. Exercise: pscan

4.6.5. Multiple Sequence Analysis

4.6.6. Exercise: Retrieving a Set of Sequences

4.6.7. Exercise: emma

4.6.8. Exercise: prettyplot

4.6.9. Profiles

4.6.10. Exercise: prophecy

4.6.11. Exercise: prophet

4.7. Report Formats

4.8. Conclusions

4.8.1. Exercise: tfm