EMBOSS Users Guide
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EMBOSS Users Guide

Practical Bioinformatics

Mr. Peter Rice

Group Leader
EMBL European Bioinformatics Institute

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Dr. Alan Bleasby

Senior Scientific Officer
EMBL European Bioinformatics Institute

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Dr. Jon Ison

Senior Scientific Officer
EMBL European Bioinformatics Institute

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Lisa Mullan

Guy Bottu

Revision History
August 2009The EMBOSS Developers
Version 1

Table of Contents

Acknowledgements
1. EMBOSS Acknowledgements
1.1. Funding Bodies
1.2. Contributors
2. EMBOSS Users Guide Acknowledgements
Preface
1. Introduction to EMBOSS
2. Using EMBOSS
3. About the Authors
4. How To Cite EMBOSS
Conventions used in the Manual
1. Command Line Sessions and Commands
2. Program Listings and Code
3. Other Conventions
4. Special Text Blocks
Welcome to the EMBOSS Users Manual
1. Chapter 1. Background to EMBOSS
2. Chapter 2. Basic Set-up and Maintenance
3. Chapter 3. Getting Started
4. Chapter 4. Tutorial
5. Chapter 5. File Formats
6. Chapter 6. The EMBOSS Command Line
7. Chapter 7. Interfaces
8. Chapter 8. Using EMBOSS under wEMBOSS
9. Chapter 9. Using EMBOSS under Jemboss
10. Appendix A. File Format Reference
11. Appendix B. Application Reference
12. Appendix C. Command-line Qualifier Reference
13. Appendix D. Resources
1. Background to EMBOSS
1.1. History
1.2. EMBOSS Developers
1.3. Key Features
1.3.1. General Features
1.3.1.1. Open source
1.3.1.2. Stable licensing
1.3.1.3. UNIX command line
1.3.1.4. Command line validation
1.3.1.5. Data in any common format
1.3.1.6. No sequence length limit
1.3.1.7. Availability and distribution
1.3.1.8. Quality assurance
1.3.2. Features for Users of EMBOSS
1.3.2.1. Simple site configuration
1.3.2.2. Support for local databases
1.3.2.3. Remote data servers
1.3.2.4. Support for users of EMBOSS
1.3.2.5. Functionality and integration
1.3.2.6. Interfaces
2. Basic Set-up and Maintenance
2.1. Supported Platforms
2.2. Hardware Requirements
2.3. Software Requirements
2.3.1. GNU Tools
2.3.2. EMBOSS Dependencies
2.3.3. EMBASSY Dependencies
2.4. Software Releases
2.4.1. Stable Releases
2.4.1.1. EMBOSS Stable Release
2.4.1.2. EMBASSY Stable Releases
2.4.1.3. Release Dates and Version Numbers
2.4.1.4. Log File of Changes
2.4.2. Developers (CVS) Release
2.5. Downloading the Stable Release
2.5.1. Downloading via the EMBOSS Website
2.5.2. Downloading via Anonymous FTP
2.5.2.1. Unpacking EMBOSS and EMBASSY Packages
2.6. Package Structure
2.6.1. Major Components
2.6.2. Sub-components
2.6.3. Differences between CVS and Stable Versions
2.7. Installation
2.7.1. Overview of the Installation Process
2.7.2. Configuration
2.7.3. Compilation
2.7.4. Setting your PATH
2.7.5. Testing all is Well
2.7.6. Database Setup
2.7.7. Installing EMBASSY Packages
2.7.7.1. Stable Release
2.8. Maintenance
2.8.1. Using CVS to Update
2.8.2. Bug-fix Replacement Files
2.8.3. Patch Files
2.8.4. Automated Installation of EMBOSS and EMBASSY
2.8.5. Automated Database Updating
3. Getting Started
3.1. Application Documentation
3.1.1. Online Documentation
3.1.1.1. Application Groups
3.1.1.2. EMBASSY Packages
3.1.1.3. Applications
3.1.2. AJAX Command Definition (ACD) Language
3.1.3. Interfaces
3.2. Navigating the Application Documentation
3.2.1. Navigating the Tabular Documentation
3.2.2. Sections in the Application Documentation
3.3. How to Contribute
3.3.1. EMBOSS Coordination Meetings
3.3.2. Collaborations
3.4. Project Mailing Lists
3.4.1. User Mailing List
3.4.2. Developer Mailing List
3.4.3. Announcements Mailing List
3.4.4. Mail Archives
3.4.4.1. User Mailing List Archive
3.4.4.2. Developer Mailing List Archive
3.5. How to Get Help
3.5.1. EMBOSS Documentation
3.5.2. EMBOSS Frequently Asked Questions
3.5.3. Asking for Help
3.5.3.1. Before you Send a Request for Support
3.5.3.2. How to Write a Request for Support
3.5.4. Suggesting New Features and Applications
3.6. Reporting Bugs and Problems
3.6.1. Where to Send a Bug Report
3.6.2. Before you Send a Bug Report
3.6.3. How to Write a Bug Report
3.7. EMBOSS Training
3.7.1. EMBOSS Tutorial
3.7.2. EMBOSS Developers Course
3.7.3. EMBOSS Workshops
4. EMBOSS User Tutorial
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
5. File Formats
5.1. Introduction
5.2. Introduction to Sequence Formats
5.2.1. What is a Sequence Format?
5.2.2. Supported Sequence Formats
5.2.3. Contents of a Sequence Entry
5.2.3.1. Identification
5.2.3.2. Bibliographic Information
5.2.3.3. Annotation and Features
5.2.3.4. The Sequence
5.2.4. Specifying Sequences on the Command Line
5.2.5. Applications for Basic Sequence Manipulation
5.3. Introduction to Feature Formats
5.3.1. What is a Feature?
5.3.2. Supported Feature Formats
5.3.3. How are Features Stored ?
5.3.4. Applications for Features
5.3.5. Specifying Features on the Command line
5.4. Introduction to Alignment Formats
5.4.1. What is an Alignment Format?
5.4.2. Supported Alignment Formats
5.4.3. Contents of an Alignment File
5.4.4. Specifying Alignments on the Command Line
5.4.5. Applications for Sequence Alignment
5.5. Introduction to Report Formats
5.5.1. What is a Report Format?
5.5.2. Supported Report Formats
5.5.3. Inside a Report
5.5.4. Specifying Reports on the Command line
5.5.5. Applications that use Reports
6. The EMBOSS Command Line
6.1. Introduction to the EMBOSS Command Line
6.1.1. Finding and Running EMBOSS Applications
6.1.2. Application Options
6.1.3. Parameters and Qualifiers
6.1.4. Datatype-specific Qualifiers
6.1.4.1. Multiple Qualifiers
6.1.4.2. Numbering Qualifiers
6.1.5. Global Qualifiers
6.1.6. Command line Styles
6.1.7. Environment Variables
6.2. Specifying Values for Application Options
6.2.1. General Rules
6.2.2. Simple ACD Datatypes
6.2.2.1. Primitive Datatypes
6.2.2.2. Other Simple Datatypes
6.2.3. Input ACD Datatypes
6.2.3.1. Sequence Input
6.2.3.2. Feature Input
6.2.3.3. Files and Directories
6.2.3.4. Data Files
6.2.3.5. Datatypes for phylipnew EMBASSY Package
6.2.3.6. Other Biological Inputs
6.2.4. Output ACD Datatypes
6.2.4.1. Sequence Output
6.2.4.2. Features
6.2.4.3. Alignments
6.2.4.4. Output Files and Directories
6.2.4.5. Output Data Files
6.2.4.6. Datatypes for phylipnew EMBASSY Package
6.2.4.7. Other Biological Outputs
6.2.4.8. Report Output
6.2.5. Selection ACD Datatypes
6.2.5.1. list
6.2.5.2. selection
6.2.6. Graphics ACD Datatypes
6.2.6.1. graph
6.2.6.2. xygraph
6.3. Global Command Line Qualifiers
6.3.1. Introduction
6.3.2. Description of Global Qualifiers
6.3.2.1. -auto
6.3.2.2. -debug
6.3.2.3. -filter
6.3.2.4. -help
6.3.2.5. -options
6.3.2.6. -stdout
6.3.2.7. -warning, -error, -fatal
6.3.3. Global Qualifiers and Environment Variables
6.3.3.1. Negation
6.4. Datatype-specific Command Line Qualifiers
6.4.1. Introduction
6.4.2. Sequences
6.4.2.1. Sequence Input
6.4.2.2. Sequence Output
6.4.3. Sequence Features
6.4.3.1. Feature Input
6.4.3.2. Feature Output
6.4.4. Sequence Alignments
6.4.4.1. Specifying the Alignment File Format and Name
6.4.5. General Input
6.4.6. Patterns
6.4.6.1. Regular Expressions
6.4.6.2. Sequence Patterns
6.4.7. General Output
6.4.7.1. General Output
6.4.7.2. Output Files
6.4.8. Application Report Output
6.4.8.1. Usage Examples
6.5. Graphical Output
6.5.1. Description of Qualifiers
6.5.1.1. Usage Examples
6.6. The Uniform Sequence Address (USA)
6.6.1. Introduction
6.6.2. USA Syntax
6.6.2.1. Sequence
6.6.2.2. Format
6.6.2.3. ListFileName
6.6.2.4. DatabaseName
6.6.2.5. FileName
6.6.2.6. Entry
6.6.2.7. SearchField
6.6.2.8. Word
6.6.2.9. Program and ProgramParameters
6.6.2.10. [start : end : reverse]
6.6.3. Specifying the Format
6.6.4. Specifying a Database
6.6.4.1. Database Name
6.6.4.2. Database Entry
6.6.4.3. Set of Database Entries
6.6.4.4. Restrictions on Accessing Databases
6.6.5. Specifying a Sequence File
6.6.5.1. Multiple Sequence Files
6.6.5.2. Specifying One or More File Entries
6.6.5.3. Specifying a Set of Files
6.6.6. Specifying a Listfile
6.6.7. Specifying a Sequence "As Is"
6.6.8. Applications
6.6.9. Specifying Search Fields
6.6.9.1. ACC and ID
6.6.9.2. ORG, KEY and DES
6.6.9.3. SV
6.6.9.4. GI Number
6.6.9.5. Start, End, Reverse
6.6.10. USA Summary
6.6.10.1. USA Examples
6.7. The Uniform Feature Object (UFO)
7. Interfaces
7.1. Introduction
7.1.1. Types of EMBOSS Interfaces
7.1.2. Selecting an Interface
7.2. Command Line Interface
7.3. Web Interfaces
7.3.1. wEMBOSS
7.3.2. WebLab
7.3.3. EMBOSS Explorer
7.3.4. W2H
7.3.5. SRSWWW
7.3.6. Biomanager
7.3.7. BioNavigator
7.3.8. Spinet
7.4. Graphical User Interfaces (GUIs)
7.4.1. Jemboss
7.4.2. Staden
7.4.3. CoLiMate
7.4.4. Kaptain
7.4.5. kemboss
7.4.6. Geneious
7.5. Workflow Interfaces
7.5.1. Taverna
7.5.2. metalife
7.5.3. Pipeline Pilot
7.5.4. BioWBI and WsBAW
7.5.5. G-Pipe
7.5.6. Mobyle
7.6. Other Interfaces
7.6.1. Utopia
7.6.2. Chipster
7.6.3. emnu
7.6.4. MolTalk
8. Using EMBOSS under WEMBOSS
8.1. Introduction
8.2. Managing Projects and Files
8.3. Running programs
8.3.1. Managing Old Outputs
8.3.2. Time-consuming Programs
8.4. Handling Input and Output
8.4.1. Handling Sequences
8.4.2. Handling Graphical Output
8.4.3. Handling Various Kinds of Input/Output Data
8.5. Plug-ins and Applets
8.6. Bugs and Fixes
8.7. wEMBOSS Tutorial
8.7.1. Exercise : Starting up wEMBOSS, creating a "project", running a program
8.7.2. Exercise : Accessing "public" databanks, using the sequence selectors, managing graphical output
8.7.3. Exercise : running a program on multiple sequences, using the output of one program as input of another, using plug-ins and applets
9. Using EMBOSS under JEMBOSS
9.1. Diving In At The Deep End
9.2. Getting Started
9.2.1. Software Requirements
9.2.2. Microsoft Desktop
9.2.3. Apple Macintosh
9.2.4. Unix Platform
9.2.5. Local Installation
9.2.6. Remote Installation
9.2.7. Jemboss Session
9.2.8. Session-specific Information
9.2.9. The Jemboss Windows
9.2.9.1. Main Jemboss Window
9.2.9.2. File Managers
9.2.9.3. Results Managers
9.2.9.4. Text Editors
9.2.10. Settings
9.2.11. Proxies
9.2.12. Servers
9.3. File Management
9.3.1. Local File Management
9.3.2. Home Directory
9.3.3. Working Directory
9.3.4. Move Up a Directory
9.3.5. Creating Data Files in Jemboss
9.3.5.1. Saving Analysis Results
9.3.5.2. Re-writing a File with New Data
9.3.5.3. Moving a File from a Location on the Desktop Computer
9.3.5.4. Drag and Drop from Remote File Manager
9.3.6. File Manipulation
9.3.7. New Folder Creation
9.3.8. Re-locating Files
9.3.9. Rename
9.3.10. Delete
9.3.11. De-select All
9.3.12. Refresh
9.3.13. Open With
9.3.14. Remote File management
9.3.15. EMBOSS Results
9.3.16. Moving Data between File Managers
9.4. Data Analysis
9.4.1. Programme Selection
9.4.2. Program Categories
9.4.3. Favourites
9.4.4. Alphabetical Program List
9.4.5. Go To Box
9.4.6. Input Section
9.4.6.1. Features
9.4.7. File Input
9.4.7.1. File/Database Entry
9.4.7.2. Browse Files
9.4.7.3. Local Files
9.4.7.4. Remote Files
9.4.7.5. Uniform Sequence Address
9.4.7.6. Paste
9.4.7.7. List of Files
9.4.8. Input Sequence Options
9.4.9. Databases Available
9.4.10. Sequence Format
9.4.11. Begin/End
9.4.12. Reverse Complement
9.4.13. Nucleotide/ Protein
9.4.14. Upper/Lower Case
9.4.15. UFO Features
9.4.16. Load Sequence Attributes
9.4.17. Parameter Selection
9.4.18. Output Section
9.4.19. Output Sequence Options
9.4.20. Sequence Format
9.4.21. Filename Extension
9.4.22. Base File Name
9.4.23. Features Format
9.4.24. Features Filename
9.4.25. Sequence Format
9.4.26. Graphical Format
9.4.27. PNG Graphics
9.4.28. Jemboss Graphics
9.4.29. Graph Options
9.4.30. Main Title
9.4.31. Axis number format
9.4.32. Ticks
9.4.33. Axis Labels
9.4.34. Graph Formatting
9.4.35. Saving Jemboss Graphics
9.4.36. Advanced Parameter Selection
9.4.37. Program run options
9.4.38. Interactive
9.4.39. Batch
9.5. Saving Results
9.5.1. Saving locally
9.5.2. Saved Results: Interactive mode
9.5.3. Saved Results: Batch Mode
9.5.4. Saving remotely
9.5.5. Analysis Run Autosave
9.5.6. Local Autosave
9.5.7. Remote Autosave
9.6. Results Retrieval
9.6.1. Retrieving Interactive Results
9.6.2. Retrieving Batch Results
9.6.3. Job Manager
9.6.4. Current Sessions Results
9.6.5. Display Results
9.6.6. Delete Results
9.6.7. Refresh Icon
9.6.8. Retrieving Saved Results
9.6.8.1. Saved Results Window
9.6.8.2. Local Results
9.6.8.3. Remote Results
9.6.8.4. Results in remote file manager
9.6.8.5. Results Manager
9.6.8.6. Delete
9.6.8.7. Edit Notes
9.6.8.8. Display
9.7. Customisation
9.7.1. Directory location
9.7.2. Programme Selection
9.7.3. Input/Output Options
9.7.3.1. Sequence Input
9.7.3.2. Adding Sequences
9.7.3.3. Deleting Sequences
9.7.3.4. Parameter behaviour
9.7.3.5. Text Output
9.7.4. Job Manager Update frequency
9.7.5. Calculate Dependencies
9.7.6. Proxy and Server Settings
9.8. Utilities
9.8.1. Jemboss Alignment Editor (JAE)
9.8.1.1. Sequence Manipulation
9.8.1.2. Sequence Manipulation Menu
9.8.1.3. Delete
9.8.1.4. Reverse Complement
9.8.1.5. Trim Sequences
9.8.1.6. Insert Annotation Sequence
9.8.1.7. Display Manipulation
9.8.1.8. Find Pattern
9.8.1.9. Matrix Display
9.8.1.10. Colour Display
9.8.1.11. Colour by Property
9.8.1.12. Colour Identical matches
9.8.1.13. Identity Number
9.8.1.14. Threshold for Positive Matches
9.8.1.15. Data Display
9.8.1.16. Consensus Sequence
9.8.1.17. Consensus Plot
9.8.1.18. Identity Table
9.8.1.19. Sort by ID
9.8.1.20. Save
9.8.1.21. Print
9.8.2. DNA Editor
9.8.2.1. Data Input
9.8.2.2. DNA Viewer
9.8.2.3. DNA Wizard
9.8.2.4. DNA Attributes
9.8.2.5. Tick Marks
9.8.2.6. Genetic Features
9.8.2.7. Restriction Enzymes
9.8.2.8. Print
9.8.3. JALVIEW
9.9. Documentation
9.9.1. Jemboss User Guide
9.9.2. Application Documentation
9.9.3. Version Number
9.9.4. Tooltips
9.9.4.1. Mouseover Tips
9.9.4.2. Static Tips
9.10. Troubleshooting
A. File Format Reference
A.1. Supported Sequence Formats
A.1.1. ABI Trace
A.1.2. ACEDB
A.1.3. ASN1
A.1.4. Asis
A.1.5. Clustal
A.1.6. CODATA
A.1.7. DAS
A.1.8. DAS DNA
A.1.9. Debug
A.1.10. EMBL
A.1.11. Experiment (Staden)
A.1.12. FASTA
A.1.13. FASTA (GCG)
A.1.14. FASTA (Pearson)
A.1.15. FASTA (with accession)
A.1.16. FASTA (database and identifier)
A.1.17. FASTA (GI style)
A.1.18. FASTA (NCBI style)
A.1.19. Fastq
A.1.20. Fastq (Illumina)
A.1.21. Fastq (Sanger)
A.1.22. Fastq (Solexa)
A.1.23. Fitch
A.1.24. GCG 8, GCG 9.x and 10.x
A.1.25. GenBank
A.1.26. GenPept
A.1.27. GFF3
A.1.28. GFF2
A.1.29. Hennig86
A.1.30. Intelligenetics
A.1.31. Jackknifer
A.1.32. Jackknifer (non-interleaved)
A.1.33. MASE
A.1.34. MEGA
A.1.35. MEGA (non-interleaved)
A.1.36. MSF
A.1.37. NBRF / PIR
A.1.38. NEXUS / PAUP (interleaved)
A.1.39. NEXUS / PAUP (non-interleaved)
A.1.40. PDB
A.1.41. PDB (nucleotide)
A.1.42. Pfam/Stockholm
A.1.43. PHYLIP (interleaved)
A.1.44. PHYLIP (non-interleaved)
A.1.45. Raw
A.1.46. RefseqP
A.1.47. SELEX
A.1.48. Staden (obsolete)
A.1.49. Strider
A.1.50. SwissProt
A.1.51. Text/Plain
A.1.52. Treecon
A.2. Supported Feature Formats
A.2.1. DASGFF
A.2.2. EMBL, GenBank, DDBJ
A.2.3. GFF3
A.2.4. GFF2
A.2.5. PIR/NBRF
A.2.6. SwissProt
A.3. Supported Alignment Formats
A.3.1. FASTA
A.3.2. Markx0
A.3.3. Markx1
A.3.4. Markx2
A.3.5. Markx3
A.3.6. Markx10
A.3.7. Match
A.3.8. MSF
A.3.9. Multiple
A.3.10. Pair
A.3.11. Score
A.3.12. Simple
A.3.13. SRS
A.3.14. SRS Pair
A.3.15. TCOFFEE
A.3.16. Trace (debugging only)
A.4. Supported Report Formats
A.4.1. DAS GFF Feature Table
A.4.2. Dbmotif
A.4.3. Debug report format
A.4.4. Diffseq
A.4.5. EMBL Feature Table
A.4.6. FeatTable
A.4.7. Genbank Feature Table
A.4.8. GFF Feature Table
A.4.9. Listfile
A.4.10. Motif
A.4.11. Nametable
A.4.12. PIR Feature Table
A.4.13. Regions
A.4.14. SeqTable
A.4.15. SRS
A.4.16. SRS Simple
A.4.17. SwissProt Feature Table
A.4.18. Tab-delimited Format
A.4.19. Table
A.4.20. TagSeq
A.4.21. Trace Feature Table (debugging only)
B. Applications and Packages Reference
B.1. Applications and Packages Documentation
B.1.1. Online Documentation
B.1.1.1. Application Groups
B.1.1.2. EMBASSY Packages
B.1.1.3. Application Documentation
B.2. Application Groups (release R6)
B.3. EMBASSY Packages (release R6)
B.4. EMBOSS Applications (release R6)
B.5. EMBASSY Applications (release R6)
B.6. All Applications (by group)
B.6.1. Applications in group Acd
B.6.2. Applications in group Alignment:consensus
B.6.3. Applications in group Alignment:differences
B.6.4. Applications in group Alignment:dot plots
B.6.5. Applications in group Alignment:global
B.6.6. Applications in group Alignment:local
B.6.7. Applications in group Alignment:multiple
B.6.8. Applications in group Display
B.6.9. Applications in group Edit
B.6.10. Applications in group Enzyme kinetics
B.6.11. Applications in group Feature tables
B.6.12. Applications in group Information
B.6.13. Applications in group Nucleic:2d structure
B.6.14. Applications in group Nucleic:codon usage
B.6.15. Applications in group Nucleic:composition
B.6.16. Applications in group Nucleic:cpg islands
B.6.17. Applications in group Nucleic:gene finding
B.6.18. Applications in group Nucleic:motifs
B.6.19. Applications in group Nucleic:mutation
B.6.20. Applications in group Nucleic:primers
B.6.21. Applications in group Nucleic:profiles
B.6.22. Applications in group Nucleic:repeats
B.6.23. Applications in group Nucleic:restriction
B.6.24. Applications in group Nucleic:transcription
B.6.25. Applications in group Nucleic:translation
B.6.26. Applications in group Phylogeny:molecular sequence
B.6.27. Applications in group Protein:2d structure
B.6.28. Applications in group Protein:3d structure
B.6.29. Applications in group Protein:composition
B.6.30. Applications in group Protein:motifs
B.6.31. Applications in group Protein:mutation
B.6.32. Applications in group Protein:profiles
B.6.33. Applications in group Utils:database creation
B.6.34. Applications in group Utils:database indexing
B.6.35. Applications in group Utils:misc
B.6.36. Applications in group Distance matrix
B.6.37. Applications in group HMM
B.6.38. Applications in group RNA folding
B.6.39. Applications in group Discrete characters
B.6.40. Applications in group Tree drawing
B.6.41. Applications in group Menus
B.6.42. Applications in group Test
B.6.43. Applications in group Continuous characters
B.6.44. Applications in group Transcription
B.6.45. Applications in group Gene frequencies
B.6.46. Applications in group Phylogeny:Consensus
B.7. GCG to EMBOSS Comparison
C. Command-line Qualifier Reference
C.1. Global Qualifiers
C.2. Datatype-specific Qualifiers
C.2.1. Sequence Input
C.2.2. Sequence Output
C.2.3. Features
C.2.4. Alignments
C.2.5. Patterns
C.2.6. Outputs
C.2.7. Reports
C.2.8. Graphics
D. Resources
D.1. EMBOSS Servers and Portals
D.1.1. EMBOSS Portals
D.1.2. EMBOSS Servers
D.1.2.1. Servers based on EMBOSS Explorer
D.1.3. Other Servers

List of Tables

2.1. EMBOSS Software Requirements
2.2. EMBASSY Software Requirements
5.1. Input sequence formats
5.2. Output sequence formats
5.3. Input feature formats
5.4. Output feature formats
5.5. Alignment formats
5.6. Report formats
6.1. Global Qualifiers
6.2. Environment variables associated with global qualifiers.
6.3. Sequence Retrieval Search Fields
6.4. Database Search Fields
8.1. Plug-ins and Applets
9.1. Troubleshooting Jemboss
B.1. Application Groups (release R6)
B.2. EMBASSY Packages (release R6)
B.3. EMBOSS Applications (release R6)
B.4. EMBASSY Applications (available alongside EMBOSS release R6)
B.5. Applications in group Acd
B.6. Applications in group Alignment:consensus
B.7. Applications in group Alignment:differences
B.8. Applications in group Alignment:dot plots
B.9. Applications in group Alignment:global
B.10. Applications in group Alignment:local
B.11. Applications in group Alignment:multiple
B.12. Applications in group Display
B.13. Applications in group Edit
B.14. Applications in group Enzyme kinetics
B.15. Applications in group Feature tables
B.16. Applications in group Information
B.17. Applications in group Nucleic:2d structure
B.18. Applications in group Nucleic:codon usage
B.19. Applications in group Nucleic:composition
B.20. Applications in group Nucleic:cpg islands
B.21. Applications in group Nucleic:gene finding
B.22. Applications in group Nucleic:motifs
B.23. Applications in group Nucleic:mutation
B.24. Applications in group Nucleic:primers
B.25. Applications in group Nucleic:profiles
B.26. Applications in group Nucleic:repeats
B.27. Applications in group Nucleic:restriction
B.28. Applications in group Nucleic:transcription
B.29. Applications in group Nucleic:translation
B.30. Applications in group Phylogeny:molecular sequence
B.31. Applications in group Protein:2d structure
B.32. Applications in group Protein:3d structure
B.33. Applications in group Protein:composition
B.34. Applications in group Protein:motifs
B.35. Applications in group Protein:mutation
B.36. Applications in group Protein:profiles
B.37. Applications in group Utils:database creation
B.38. Applications in group Utils:database indexing
B.39. Applications in group Utils:misc
B.40. Applications in group Distance matrix
B.41. Applications in group HMM
B.42. Applications in group RNA folding
B.43. Applications in group Discrete characters
B.44. Applications in group Tree drawing
B.45. Applications in group Menus
B.46. Applications in group Test
B.47. Applications in group Continuous characters
B.48. Applications in group Transcription
B.49. Applications in group Gene frequencies
B.50. Applications in group Phylogeny:Consensus
B.51. Table of equivalent GCG / EMBOSS programs
C.1. Global Qualifiers
C.2. Sequence Reading Qualifiers
C.3. Sequence Writing Qualifiers.
C.4. Feature Qualifiers
C.5. Alignment qualifiers
C.6. Pattern qualifiers
C.7. Output qualifiers.
C.8. Report Qualifiers
C.9. Graph qualifiers.
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   Acknowledgements