EMBOSS user's guide : practical bioinformatics
Contents
1. management 189 Local file management 189 Home directory 189 Working directory 190 Move up a directory 190 Creating data files in Jemboss 190 9 3 6 9 3 7 9 3 8 9 3 9 9 3 10 9 3 11 9 3 12 9 3 13 9 3 14 9 3 15 9 3 16 9 4 9 4 1 9 4 2 9 4 3 9 4 4 9 4 5 9 4 6 9 4 7 9 4 8 9 4 9 9 4 10 9 4 11 9 4 12 9 4 13 9 4 14 9 4 15 9 4 16 9 4 17 9 4 18 9 4 19 9 4 20 9 4 21 9 4 22 9 4 23 9 4 24 9 4 25 9 4 26 9 4 27 9 4 28 9 4 29 9 4 30 9 4 31 9 4 32 9 4 33 9 4 34 9 4 35 CONTENTS File manipulation 191 New folder creation I91 Re locating files 192 Rename 192 Delete 192 De select all 192 Refresh 193 Open with 193 Remote file management 193 EMBOSS results 193 Moving data between file managers 194 Data analysis 194 Program selection 194 Program categories 194 Favourites 194 Alphabetical program list 195 Go To box 195 Input section 195 File input 195 Input sequence options 196 Databases available 197 Sequence format 197 Begin end 197 Reverse complement 197 Nucleotide protein 197 Upper lower case 197 UFO features 197 Load sequence attributes 198 Parameter selection 198 Output section 198 Output sequence options 199 Sequence format 199 Filename extension 199 Base filename 199 Features format 199 Features filename 200 Sequence format 200 Graphical format 200 PNG graphics 200 Jemboss graphics 200 Graph options 201 Main title 201 Axis number format 201 Ticks 201 Axis labels 22. 01 Graph formatting 201 Saving Jemboss graphics 202 XI 9 4 36 9 4 37 9 4 38 9 4 39 9 5 9 5 1 9 5 2 9 5 3 9 5 4 9 5 5 9 5 6 9 5 7 9 6 9 6 1 9 6 2 9 6 3 9 6 4 9 6 5 9 6 6 9 6 7 9 6 8 9 7 9 7 1 9 7 2 9 7 3 9 7 4 9 7 5 9 7 6 9 8 9 8 1 1 8 2 1 8 3 2 9 9 9 1 9 9 2 9 9 3 9 9 4 9 10 CONTENTS Advanced parameter selection 202 Program run options 202 Interactive mode 202 Batch mode 202 Saving results 203 Saving locally 203 Saved results interactive mode 203 Saved results batch mode 204 Saving remotely 204 Analysis run autosave 205 Local autosave 205 Remote autosave 205 Results retrieval 206 Retrieving interactive results 206 Retrieving batch results 206 Job Manager 206 Current Sessions Results 206 Display results 207 Delete results 207 Refresh icon 207 Retrieving saved results 208 Customisation 211 Directory location 211 Program selection 212 Input output options 212 Job Manager update frequency 214 Calculate dependencies 214 Proxy and server settings 214 Utilities 214 Jemboss Alignment Editor JAE 214 DNA Editor 220 JALVIEW 223 Documentation 223 Jemboss user guide 223 Application documentation 223 Version number 224 Tooltips 224 Troubleshooting 224 Appendix A File format reference 226 A l A 1 1 A 1 2 A 1 3 A 1 4 A 1 5 A 1 6 Supported sequence formats 226 ABI trace 226 ACEDB 226 ASNI 227 Asis 228 Clustal 228 CODATA 228 XII CONTENTS DAS 229 DASDNA 230 Debug
3. 230 EMBL 231 Experiment Staden 233 FASTA 234 FASTA GCG 234 FASTA Pearson 235 FASTA with accession 235 FASTA database and identifier 235 FASTA GI style 236 FASTA NCBI style 236 Fastq 237 Fastq Illumina 237 Fastq Sanger 237 Fastq Solexa 238 Fitch 238 GCG 8 GCG 9 x and 10 x 238 GenBank 239 GenPept 241 GFF3 242 GFF2 243 Hennig86 243 Intelligenetics 244 Jackknifer 244 Jackknifer non interleaved 245 MASE 245 MEGA 246 MEGA non interleaved 246 MSF 247 NBRF PIR 248 NEXUS PAUP interleaved 248 NEXUS PAUP non interleaved 249 PDB 250 PDB nucleotide 252 Pfam Stockholm 261 PHYLIP Gnterleaved 264 PHYLIP non interleaved 264 Raw 265 RefsegP 265 SELEX 268 Staden obsolete 269 Strider 269 SwissProt 271 Text Plain 273 Treecon 274 Supported feature formats 275 XII A 2 1 A 2 2 A 2 3 A 2 4 A 2 5 A 2 6 A 3 1 A 3 2 A 3 3 A 3 4 A 3 5 A 3 6 A 3 7 A 3 8 A 3 9 A 3 10 A 3 11 A 3 12 A 3 13 A 3 14 A 3 15 A 3 16 A 4 1 A 4 2 A 4 3 A 4 4 A 4 5 A 4 6 A 4 7 A 4 8 A 4 9 A 4 10 A 4 11 A 4 12 A 4 13 A 4 14 A 4 15 A 4 16 A 4 17 A 4 18 A 4 19 A 4 20 A 4 21 CONTENTS DASGFF 275 EMBL GenBank DDB 279 GFF3 280 GFF2 281 PIR NBRF 282 SwissProt 283 Supported alignment formats 284 FASTA 284 MarkxO 284 Markxl 285 Markx2 286 Markx3 287 Markxl10 288 Match 289 MSF 289 Multiple 290 Pair 291 Score 292 Simple 292 SRS 292 SRS Pair 293 TCOF
4. BOSS Explorer W2H 162 SRSWWW BioNavigator Spinet 163 Graphical user interfaces GUIs 163 Jemboss 164 Staden 165 CoLiMate 165 Kaptain 165 kemboss 165 Geneious 166 Workflow interfaces Taverna 167 metalife 167 Pipeline Pilot 162 163 163 166 167 CONTENTS 123 143 159 IX 7 6 4 7 6 5 7 6 6 77 7 7 1 7 7 2 7 7 3 7 8 9 2 10 9 2 11 9 2 12 9 3 9 3 1 9 3 2 9 3 3 9 3 4 9 3 5 CONTENTS BioWBI and WsBAW_ 167 G Pipe 168 Mobyle 168 Other interfaces 168 Utopia 169 emnu 169 MolTalk 169 Selecting an interface 169 Using EMBOSS under wEMBOSS 170 Introduction 170 Managing projects and files 171 Project management 172 Running programs 172 Programs 175 Handling input and output 175 Plug ins and applets 177 Bugs and fixes 178 wEMBOSS tutorial 178 Exercise Starting up WEMBOSS creating a project running a program 179 Exercise Accessing public databanks using the sequence selectors managing graphical output 179 Exercise Running a program on multiple sequences using the output of one program as input of another using plug ins and applets 180 Using EMBOSS under Jemboss 183 Diving in atthe deep end 183 Getting started 185 Software requirements 185 Microsoft desktop 186 Apple Macintosh 186 UNIX platform 186 Local installation 186 Remote installation 187 Jemboss session 187 Session specific information 187 The Jemboss windows 187 Settings 188 Proxies 189 Servers 189 File
5. EMBOSS User s Guide Mr Peter Rice EMBL European Bioinformatics Institute Dr Alan Bleasby EMBL European Bioinformatics Institute Dr Jon Ison EMBL European Bioinformatics Institute with contributions from Lisa Mullan Guy Bottu CAMBRIDGE AG UNIVERSITY PRESS Contents Acknowledgements page XVI Preface XIX Conventions XXII 1 1 1 2 1 3 1 3 1 1 3 2 2 1 2 3 2 3 1 2 3 2 2 3 3 2 4 1 2 4 2 2 5 2 5 1 2 5 2 2 6 Welcome to the EMBOSS User s Guide xxv Summary XXV Chapter 1 Background to EMBOSS xxv Chapter 2 Basic setup and maintenance XXV Chapter 3 Getting started XXV Chapter 4 Tutorial XXV Chapter 5 File formats XXV Chapter 6 The EMBOSS command line XXVI Chapter 7 Interfaces XXVI Chapter 8 Using EMBOSS under wWEMBOSS 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 XXVII Background to EMBOSS History 1 EMBOSS developers 2 Key features 3 General features 3 Features for users of EMBOSS 5 Basic setup and maintenance 7 Supported platforms 7 Hardware requirements 8 Software requirements 8 GNU tools 8 EMBOSS dependencies 8 EMBASSY dependencies 8 Software releases 9 Stable releases 9 Developer s CVS release 11 Downloading the stable release 11 Downloading via the EMBOSS website 11 Downloading via anonymo
6. FEE 294 Trace debugging only 295 Supported report formats 295 XIV DAS GFF feature table 295 Dbmotif 297 Debug report format 298 Diffseq 298 EMBL feature table 300 FeatTable 300 GenBank feature table 301 GFF feature table 301 Listfile 301 Motif 302 Nametable 304 PIR feature table 306 Regions 306 SeqTable 307 SRS 308 SRS Simple 310 SwissProt feature table 312 Tab delimited format 312 Table 313 TagSeq 314 Trace feature table debugging only 317 CONTENTS Appendix B Applications and packages reference 3138 B 1 Applications and packages documentation 318 B 1 1 Online documentation 318 B 2 Application groups release R6 319 B 3 EMBASSY packages release R6 320 B 4 Applications 321 B 4 1 EMBOSS applications release R6 321 B 4 2 EMBASSY applications available alongside EMBOSS release R6 326 B 4 3 All applications by group 329 B 5 GCG to EMBOSS comparison 343 Appendix C Command line qualifier reference 361 C 1 Global qualifiers 361 C 2 Datatype specific qualifiers 361 C 2 1 Sequence input 361 C 2 2 Sequence output 363 C 2 3 Features 364 C 2 4 Alignments 364 C 2 5 Patterns 365 C 2 6 Outputs 365 C 2 7 Reports 368 C 2 8 Graphics 368 Appendix D Resources 369 D 1 EMBOSS servers and portals 369 D 1 1 EMBOSS portals 369 D 1 2 EMBOSS servers 369 Index 371 xv
7. d running EMBOSS applications 96 Application options 96 Command line styles 102 Environment variables 102 Specifying values for application options 102 General rules 102 Simple ACD datatypes 103 Input ACD datatypes 106 Output ACD datatypes ITI Selection ACD datatypes 114 Graphics ACD datatypes I16 Global command line qualifiers 116 Introduction 116 Description of global qualifiers 117 Global qualifiers and environment variables 121 VUI 6 4 6 4 1 6 4 2 6 4 3 6 4 4 6 4 5 6 4 6 6 4 7 6 4 8 6 5 6 5 1 6 6 1 6 6 2 6 6 3 6 6 4 6 6 5 6 6 6 6 6 7 6 6 8 6 6 9 6 6 10 6 7 7 1 7 2 7 3 7 4 7 4 1 7 4 2 7 4 3 7 4 4 7 4 5 7 4 6 7 4 7 7 5 1 7 5 2 7 5 3 7 5 4 7 5 5 7 5 6 7 6 1 7 6 2 7 6 3 Datatype specific command line qualifiers Introduction 123 Sequences 123 Sequence features 132 Sequence alignments 137 General input 139 Patterns 139 General output 140 Application report output I4I Graphical output 142 Description of qualifiers 142 The Uniform Sequence Address USA Introduction 143 USA syntax 144 Specifying the format 146 Specifying a database 147 Specifying a sequence file Specifying a listfile 151 Specifying a sequence as is 152 Applications 152 Specifying search fields USA summary 157 The Uniform Feature Object UFO 149 153 Interfaces 160 Introduction 160 Command line interfaces 160 Types of EMBOSS interfaces 161 Web interfaces I61 wEMBOSS 162 WebLab 162 EM
8. g report 35 How to write abug report 35 EMBOSS training 35 EMBOSS tutorial 36 EMBOSS developer s course 36 EMBOSS workshops 36 VI 4 1 4 2 1 4 3 4 4 1 4 5 4 5 1 4 6 4 7 4 8 4 10 4 11 4 12 4 12 1 4 12 2 4 13 4 13 1 4 14 4 14 1 4 15 4 16 4 16 1 4 16 2 4 17 4 17 1 4 18 4 19 4 20 4 20 1 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 4 27 1 4 27 2 CONTENTS EMBOSS user tutorial 37 How this tutorial is organised 37 wossname a first EMBOSS application 37 Exercise wossname 37 Working with sequences 38 Retrieving sequences from databases 39 Exercise showdb 39 segret 40 Exercise segret 40 Reading sequences from files 41 infoseq 4I Sequence annotation 42 Using multiple sequences 44 Listfiles 44 Pairwise sequence alignment 46 Dotplots 47 Exercise making a dotplot 47 Exercise examining dotplot parameters 48 Global alignment 48 Exercise needle 49 Local alignment 50 Exercise water 50 Protein analysis 52 Identifying the open reading frame ORF 52 Exercise plotorf 52 Exercise getorf 52 Translating the sequence 54 Exercise transeq 54 USA for partial sequences 55 Secondary structure prediction 55 pepinfo 56 Exercise pepinfo 56 Predicting transmembrane regions 56 Exercise tmap 56 Patterns profiles and multiple sequence alignment 58 Pattern matching 59 Exercise patmatmotifs 59 Report formats 60 Protein fingerprints 61 Exercise pscan 61 Multiple se
9. quence analysis 62 Exercise retrieving a set of sequences 63 Exercise emma 63 Exercise prettyplot 66 Profiles 67 Exercise prophecy 68 Exercise prophet 69 vit 4 28 4 28 1 5 1 5 2 5 2 1 5 2 2 5 2 3 5 2 4 5 2 5 5 3 1 5 3 2 5 3 3 5 3 4 5 3 5 5 4 5 4 1 5 4 2 5 4 3 5 4 4 5 4 5 5 5 1 5 5 2 5 5 3 5 5 4 5 5 6 1 6 1 1 6 1 2 6 1 3 6 1 4 6 2 6 2 1 6 2 2 6 2 3 6 2 4 6 2 5 6 2 6 6 3 6 3 1 6 3 2 6 3 3 CONTENTS Conclusion 69 Exercise tfm 69 File formats 70 Introduction to file formats 70 Introduction to sequence formats 71 What is a sequence format 71 Supported sequence formats 72 Contents of a sequence entry 76 Specifying sequences on the command line 80 Applications for basic sequence manipulation 81 Introduction to feature formats 82 What js a feature 82 Supported feature formats 82 How are features stored 83 Applications for features 84 Specifying features on the command line 84 Introduction to alignment formats 84 What is an alignment format 85 Supported alignment formats 86 Contents of an alignment file 87 Specifying alignments on the command line 88 Applications for sequence alignment 89 Introduction to report formats 91 What is a report format 91 Supported report formats 91 Inside a report 92 Specifying reports on the command line 94 Applications that use reports 94 The EMBOSS command line 96 Introduction to the EMBOSS command line 96 Finding an
10. us FTP 12 Package structure 14 2 6 1 2 6 2 2 6 3 2 7 2 7 1 2 7 2 2 7 3 2 7 4 2 7 5 2 7 6 2 7 7 2 8 2 8 1 2 8 2 2 8 3 2 8 4 2 8 5 3 1 3 1 1 3 1 2 3 1 3 3 2 1 3 2 2 3 3 3 3 1 3 3 2 3 4 3 4 1 3 4 2 3 4 3 3 4 4 3 5 3 5 1 3 5 2 3 5 3 3 5 4 3 6 3 6 1 3 6 2 3 6 3 3 7 1 3 7 2 3 7 3 CONTENTS Major components 14 Sub components 14 Differences between CVS and stable versions 15 Installation 16 Overview of the installation process 16 Configuration 16 Compilation 17 Setting your PATH 18 Testing all is well 18 Database setup 19 Installing EMBASSY packages 20 Maintenance 22 Using CVS to update 22 Bug fix replacement files 23 Patch files 24 Automated installation of EMBOSS and EMBASSY 25 Automated database updating 26 Getting started 28 Application documentation 28 Online documentation 28 AJAX command definition ACD language 29 Interfaces 29 Navigating the application documentation 29 Navigating the tabular documentation 29 Sections in the application documentation 29 How to contribute 30 EMBOSS coordination meetings 31 Collaborations 31 Project mailing lists 31 User mailing list 31 Developer mailing list 32 Announcements mailing list 32 Mail archives 32 How to gethelp 33 EMBOSS documentation 33 EMBOSS frequently asked questions 33 Asking forhelp 33 Suggesting new features and applications 34 Reporting bugs and problems 35 Where to senda bug report 35 Before you send a bu
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