Download EMBOSS user's guide : practical bioinformatics

EMBOSS
User's Gu
Mr Peter Rice
EMBL
European Bioinformatics
Dr Alan
Institute
Bleasby
EMBL European Bioinformatics Institute
Dr
Jon
EMBL
Ison
European
Bioinformatics Institute
with contributions from
Lisa Mullan
Guy
Bottu
CAMBRIDGE
UNIVERSITY PRESS
Contents
Acknowledgements
Preface
page
XVI
XIX
Conventions
XXII
Welcome to the EMBOSS User's Guide
Summary
Chapter 1.
Chapter 2.
Chapter 3.
Chapter 4.
xxv
XXV
Background
to
EMBOSS
XXV
Basic setup and maintenance
Getting
started
Tutorial
XXV
XXV
XXV
Chapter
5. File formats
Chapter
6. The EMBOSS command line
Chapter
Chapter
7. Interfaces
XXV
XXVI
XXVI
8. Using EMBOSS under wEMBOSS
XXVI
Chapter 9. Using EMBOSS under Jemboss xxvi
Appendix A. File format reference XXVI
Appendix B. Application reference XXVII
Appendix C. Command-line qualifier reference XXVII
Appendix D. Resources XXVH
1
Background
1.1
History
1.2
EMBOSS
1.3
Key features
to EMBOSS
developers
General features
1.3.2
Features for
2.1
2.2
2.3
2
3
1.3.1
2
3
users
of EMBOSS
Basic setup and maintenance
Supported platforms 7
Hardware requirements
8
Software requirements
8
2.3.1
GNU tools
2.3.2
EMBOSS dependencies
2.3.3
EMBASSY
2.4
2.4.1
2.4.2
i
I
5
7
8
dependencies
Software releases
9
Stable releases
9
8
8
2.5.2
Developer's (CVS) release 11
Downloading the stable release 11
Downloading via the EMBOSS website
Downloading via anonymous FTP 12
2.6
Package
2.5
2.5.1
structure
11
14
V
CONTENTS
Major components
Sub-components
2.6.1
2.6.2
Differences between CVS and stable versions
2.6.3
2.7
14
14
Installation
2.7.1
Overview of the installation process
2.7.2
2.7.4
Configuration 16
Compilation 17
Setting your PATH
2.7.5
Testing
2.7.6
Database setup
2.7.7
Installing EMBASSY packages
2.7.3
2.8
15
16
all is well
Maintenance
16
18
18
19
20
22
2.8.2
Using CVS to update 22
Bug-fix replacement files 23
2.8.3
Patch files
2.8.4
Automated installation of EMBOSS and EMBASSY
2.8.5
Automated database
2.8.1
24
started
3
Getting
3.1
Application documentation
28
3.1.1
Online documentation
3.1.2
AJAX
3.1.3
Interfaces
3.2
26
updating
28
28
command definition
(ACD) language
29
29
3.2.2
Navigating the application documentation 29
Navigating the tabular documentation 29
Sections in the application documentation
29
3.3
How to contribute
3.2.1
30
EMBOSS coordination meetings
Collaborations
31
3.3.1
3.3.2
3.4
3.4.1
3.4.2
3.4.3
Project mailing lists 31
User mailing list 31
Developer mailing list 32
Announcements mailing list
3.4.4
3.5
Mail archives
How to get
help
33
EMBOSS documentation
3.5.2
EMBOSS
3.5.4
3.6
3.6.1
33
frequently asked questions 33
Asking for help
33
Suggesting new features and applications
Reporting bugs and problems 35
Where to send a bug report
35
3.6.2
Before you send a bug report
35
How to write a bug report
35
3.6.3
3.7
32
32
3.5.1
3.5.3
31
EMBOSS training
3.7.1
EMBOSS tutorial
3.7.2
EMBOSS
3.7.3
EMBOSS
VI
35
36
developer's course
workshops 36
36
34
25
CONTENTS
tutorial
4
EMBOSS
4.1
How this tutorial is
4.2
wossname: a
4.2.1
4.3
4.4
4.4.1
4.5
4.5.1
4.6
user
Exercise:
37
organised
first EMBOSS
37
application
Working with sequences 38
Retrieving sequences from databases
Exercise: showdb
seqret
40
Exercise: seqret
40
4.9
4.10
Listfiles
4.11
Pairwise sequence alignment
4.12
Dotplots
4.8
39
39
Reading sequences from files
infoseq 41
Sequence annotation 42
Using multiple sequences 44
4.7
41
44
46
4.12.1
47
Exercise: making
4.12.2
Exercise: examining dotplot parameters
4.13
4.13.1
4.14
4.14.1
Global alignment
Exercise:
4.16
Identifying
4.16.1
4.16.2
Exercise:
partial
USA for
Secondary
4.20
pepinfo
4.21
4.21.1
4.22
4.23
4.23.1
4.24
4.25
4.25.1
4.26
4.26.1
4.26.2
4.26.3
4.27
49
50
52
54
sequences
structure
52
54
sequence
Exercise: transeq
4.19
48
50
reading frame (ORF)
plotorf 52
getorf 52
Translating the
4.18
47
the open
Exercise:
4.20.1
dotplot
48
water
Protein analysis
4.17.1
a
Exercise: needle
Local alignment
4.15
4.17
37
37
wossname
55
prediction
55
56
Exercise: pepinfo
56
Predicting transmembrane regions 56
Exercise: tmap 56
Patterns, profiles and multiple sequence alignment
Pattern matching
59
Exercise: patmatmotifs
59
Report formats 60
61
Protein fingerprints
Exercise: paean
61
Multiple sequence analysis
Exercise: retrieving a set
Exercise: emma
63
62
of sequences
Exercise: prettyplot
Profiles
58
63
66
67
4.27.1
Exercise: prophecy
4.27.2
Exercise: prophet
68
69
VII
CONTENTS
4.28
4.28.1
Conclusion
69
Exercise: tfm
69
5
File formats
70
5.1
Introduction
to
file formats
5.2
Introduction
to
sequence formats
5.2.1
What is
5.2.2
Supported
a
70
sequence format?
71
71
5.2.4
sequence formats
72
Contents of a sequence entry
76
Specifying sequences on the command line
5.2.5
Applications
5.2.3
5.3
Introduction
to
feature formats
5.3.1
What is
5.3.2
Supported
5.3.3
How are features stored ?
5.3.4
Applications for
5.3.5
5.4
a
feature?
82
feature formats
82
83
features
84
Specifying features on the command line
to alignment formats
84
What is
format?
85
Supported alignment formats
86
5.4.3
Contents of
5.5
5.5.1
an
alignment
alignment file 87
Specifying alignments on the command line
Applications for sequence alignment 89
an
Supported
5.5.3
Inside
5.5.4
Specifying
a
report formats
report
91
92
reports
Applications that
on
use
the command line
reports
The EMBOSS command line
6.1
6.1.1
Introduction
to
94
94
96
the EMBOSS command line
6.1.2
running EMBOSS applications
Application options 96
6.1.3
Command line styles
6.1.4
Environment variables
6.2
6.2.1
6.2.2
6.2.3
6.2.4
6.2.5
6.2.6
6.3
Finding
and
96
102
Specifying values for application options
General rules
96
102
102
102
Simple ACD datatypes 103
Input ACD datatypes 106
Output ACD datatypes ill
Selection ACD datatypes
114
Graphics ACD datatypes 116
116
Global command line qualifiers
116
6.3.1
Introduction
6.3.2
Description of global qualifiers 117
Global qualifiers and environment variables
6.3.3
88
Introduction to report formats
91
What is a report format?
91
5.5.2
.5.5
84
Introduction
5.4.2
5.4.5
81
82
5.4.1
5.4.4
80
for basic sequence manipulation
VIII
121
CONTENTS
6.4
Datatype-specific command line qualifiers
6.4.1
Introduction
6.4.2
6.4.5
Sequences 123
Sequence features
132
Sequence alignments 137
General input
139
6.4.6
Patterns
6.4.7
General output
6.4.3
6.4.4
6.4.8
6.5
6.5.1
6.6
139
140
Application report output 141
Graphical output 142
Description of qualifiers 142
The Uniform Sequence Address (USA)
6.6.1
Introduction
6.6.2
USA syntax
6.6.3
Specifying the format 146
Specifying a database 147
Specifying a sequence file
149
Specifying a listfile 151
6.6.4
6.6.5
6.6.6
144
Specifying
6.6.8
6.6.9
Applications 152
Specifying search fields
6.6.10
USA summary
a
sequence'as is1
The Uniform Feature
7
Interfaces
7.1
Introduction
7.2
Command line interfaces
7.3
Types
7.4
Web interfaces
160
7.4.3
EMBOSS Explorer
7.4.4
W2H
7.4.5
SRSWWW
7.5.4
162
162
162
162
163
BioNavigator 163
Spinet 163
Graphical user interfaces (GUIs)
Jemboss 164
Staden
165
CoLiMate
165
165
Kaptain
7.5.5
kemboss
7.5.6
Geneious
7.6
161
161
WebLab
7.5.3
160
of EMBOSS interfaces
wEMBOSS
7.5.2
159
160
7.4.2
7.5.1
153
Object (UFO)
7.4.1
7.5
152
157
6.7
7.4.7
143
143
6.6.7
7.4.6
123
123
163
165
166
Workflow interfaces
7.6.1
Taverna
7.6.2
metalife
7.6.3
Pipeline Pilot
166
167
167
167
IX
CONTENTS
7.6.4
BioWBI and WsBAW
7.6.5
G-Pipe
Mobyle
7.6.6
7.7
168
Other interfaces
168
7.8
169
169
MolTalk
169
Selecting an interface
8
Using EMBOSS under
8.1
Introduction
8.2
Managing projects and files
Project management 172
Running programs 172
Programs 175
7.7.1
7.7.2
7.7.3
8.3
8.3.1
8.4
167
168
Utopia
emnu
Handling
8.4.1
169
wEMBOSS
170
170
input
and output
8.5
Plug-ins and applets
8.6
Bugs
8.7
wEMBOSS tutorial
and fixes
171
175
177
178
178
Exercise: Starting up wEMBOSS, creating
8.7.1
program
a
'project', running
a
179
8.7.2
Exercise: Accessing 'public' databanks, using the sequence selectors,
8.7.3
managing graphical output 179
Exercise: Running a program on multiple sequences, using the output
180
program as input of another, using plug-ins and applets
9.1
Using EMBOSS under Jemboss
Diving in at the deep end 183
9.2
Getting
9
started
183
185
requirements
9.2.1
Software
9.2.2
Microsoft desktop
9.2.3
9.2.4
Apple Macintosh
UNIX platform
9.2.5
Local installation
9.2.6
Remote installation
185
186
186
186
186
9.2.10
187
Jemboss session 187
Session-specific information 187
The Jemboss windows
187
Settings 188
9.2.11
Proxies
9.2.12
Servers
9.2.7
9.2.8
9.2.9
9.3
9.3.1
189
189
File management
189
Local file management
189
9.3.2
Home directory
9.3.3
Working directory 190
Move up a directory 190
Creating data files in Jemboss
9.3.4
9.3.5
X
189
190
of
one
CONTENTS
manipulation
9.3.6
File
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
9.4
Moving
191
191
192
192
192
192
193
193
data between file managers
Data analysis
Program selection 194
Program categories 194
9.4.3
Favourites
194
9.4.4
Alphabetical
program list
9.4.5
Go To box
9.4.6
9.4.8
Input section 195
File input
195
Input sequence options
9.4.9
Databases available
9.4.10
9.4.11
Sequence format
Begin/end 197
9.4.12
Reverse complement
9.4.13
9.4.14
Nucleotide/protein 197
Upper/lower-case 197
9.4.15
UFO features
9.4.16
Load sequence attributes
9.4.17
Parameter selection
9.4.18
9.4.20
Output section 198
Output sequence options
Sequence format 199
9.4.21
Filename extension
9.4.22
Base filename
9.4.23
Features format
9.4.24
Features filename
9.4.25
Sequence format
9.4.26
9.4.29
Graphical format 200
200
PNG graphics
Jemboss graphics 200
Graph options 201
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
9.4.7
9.4.19
9.4.27
9.4.28
194
194
9.4.2
9.4.1
193
193
195
195
196
197
197
197
197
198
198
199
199
199
199
200
200
201
201
201
201
201
202
XI
CONTENTS
9.4.36
Advanced parameter selection
9.4.37
Program
9.4.38
Interactive mode
9.4.39
Batch mode
9.5
run
options
202
202
202
202
Saving results
203
Saving locally
9.5.1
9.5.2
203
Saved results: interactive mode
9.5.3
Saved results: batch mode
9.5.4
9.5.5
Saving remotely 204
Analysis run autosave
9.5.6
Local autosave
Results retrieval
205
205
Remote autosave
9.5.7
9.6
205
206
9.6.3
Retrieving interactive results
Retrieving batch results 206
Job Manager 206
9.6.4
Current Sessions Results
9.6.5
Display
9.6.6
Delete results
9.6.7
Refresh icon
9.6.1
9.6.2
9.7
results
Retrieving
9.6.8
206
206
207
207
207
saved results
Customisation
208
211
9.7.1
Directory location
211
9.7.2
Program selection
212
9.7.3
Input/output options 212
Job Manager update frequency
Calculate dependencies
214
Proxy and server settings 214
9.7.4
9.7.5
9.7.6
9.8
Utilities
203
204
214
214
9.8.1
Jemboss Alignment Editor QAE)
\8.2
DNA Editor
t.8.3
J.9
JALVTEW 223
Documentation 223
9.9.1
Jemboss user guide
9.9.2
Application documentation
9.9.3
Version number
9.9.4
9.10
Appendix
214
220
Tooltips 224
Troubleshooting
A
A.l
224
226
sequence formats
A.l.l
ABI trace
A.1.2
ACEDB
A. 1.3
ASN1
A. 1.4
Asis
A.1.5
Clustal
A.l.6
CODATA
223
224
File format reference
Supported
XII
223
226
226
227
228
228
228
226
CONTENTS
A. 1.7
DAS
A. 1.8
DASDNA
A. 1.9
Debug
230
A.1.10
EMBL
231
A.l.ll
Experiment (Staden)
A.1.12
FASTA
234
A.1.13
FASTA
(GCG)
A.1.14
FASTA (Pearson)
229
230
233
234
A.1.15
235
FASTA (with accession)
A.1.16
FASTA (database and identifier)
A.1.17
FASTA (GI style)
235
A. 1.24
236
FASTA (NCBIstyle)
236
Fastq 237
Fastq (Illumina) 237
Fastq (Sanger) 237
Fastq (Solexa) 238
Fitch
238
GCG 8, GCG 9.x and 10.x
238
A.1.25
GenBank
239
A. 1.26
GenPept
241
A.1.18
A.1.19
A. 1.20
A.1.21
A. 1.22
A.1.23
A. 1.27
GFF3
242
A.1.28
GFF2
243
A. 1.29
A. 1.32
Hennig86 243
Intelligenetics 244
Jackknifer 244
Jackknifer (non-interleaved)
A.1.33
MASE
A. 1.34
MEGA
A.1.35
MEGA
A.1.36
MSF
A. 1.30
A.1.31
A.1.37
245
245
246
(non-interleaved)
246
247
NBRF/PIR
A. 1.39
248
(interleaved) 248
NEXUS/PAUP (non-interleaved)
A. 1.40
PDB
A.1.41
PDB
A. 1.42
Pfam/Stockholm
A. 1.43
PHYLIP (interleaved)
A. 1.44
PHYLIP (non-interleaved)
A. 1.45
Raw
A.1.38
NEXUS/PAUP
249
250
(nucleotide)
A. 1.46
265
RefseqP 265
A. 1.47
SELEX
A. 1.48
Staden
A. 1.49
Strider
264
264
269
269
SwissProt
A.1.51
Text/Plain
A. 1.52
Treecon
Supported
252
261
268
(obsolete)
A.1.50
A.2
235
271
273
274
feature formats
275
XIII
CONTENTS
A.2.1
DASGFF
A.2.2
EMBL, GenBank, DDBJ
A.2.3
275
GFF3
280
A.2.4
GFF2
281
A.2.5
PIR/NBRF
A.2.6
SwissProt
279
282
283
Supported alignment formats
FASTA
284
A.3
A.3.1
A.3.2
MarkxO
A.3.3
Markxl
284
285
A.3.4
Markx2
286
A.3.5
Markx3
287
A.3.6
MarkxlO
A.3.7
Match
A.3.8
MSF
284
288
A.3.9
289
289
Multiple 290
A.3.10
Pair
A.3.11
Score
A.3.12
Simple
A.3.13
SRS
291
292
292
292
SRS Pair 293
TCOFFEE
294
A.3.14
A.3.15
A.3.16
Trace (debugging only)
Supported report formats
A.4
295
295
A.4.1
DAS GFF feature table
A.4.2
Dbmotif
A.4.3
Debug
Diffseq
A.4.4
A.4.5
297
report format
A.4.7
298
298
EMBL feature table
FeatTable 300
A.4.6
295
300
GenBank feature table 301
GFF feature table 301
A.4.8
A.4.9
Listfile
A.4.10
Motif
A.4.11
Nametable
301
302
A.4.12
304
P1R feature table
A.4.13
Regions
A.4.14
SeqTable
A.4.15
SRS
307
308
SRS Simple
A.4.16
A.4.17
306
306
310
A.4.18
SwissProt feature table
Tab-delimited format
A.4.19
Table
A.4.20
TagSeq
A.4.21
Trace feature table
XIV
312
312
313
314
(debugging only)
317
CONTENTS
Appendix
B
B.l
Applications and packages reference
Applications
and packages documentation
Online documentation
B. 1.1
318
(release R6)
packages (release R6)
B.2
Application
B.3
EMBASSY
B.4
Applications
groups
319
320
321
applications (release R6) 321
EMBASSY applications (available alongside EMBOSS release R6)
B.4.1
EMBOSS
B.4.2
B.4.3
All
GCG
B. 5
applications (by group) 329
to EMBOSS comparison
343
Appendix C Command line qualifier reference
361
Global qualifiers
C. 2.8
361
Datatype-specific qualifiers
Sequence input 361
Sequence output 363
Features
364
Alignments 364
Patterns
365
Outputs 365
Reports 368
Graphics 368
Appendix D
Resources
D. l
EMBOSS
C. l
C.2
C.2.1
C.2.2
C.2.3
C.2.4
C.2.5
C.2.6
C.2.7
361
369
servers and
D.l.l
EMBOSS portals
D.l.2
EMBOSS
Index
318
318
servers
portals
369
369
369
371
XV