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Geneious Prime 2020.0 User Manual

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Geneious Prime 2020.0 User Manual Geneious Prime 2020.0 User Manual Biomatters Ltd January 14, 2020 Contents 1 Getting Started7 1.1 Downloading & Installing Geneious Prime ..................... 7 1.2 Geneious Prime setup ................................. 9 1.3 Upgrading to new versions .............................. 16 1.4 Licensing......................................... 17 1.5 Troubleshooting..................................... 19 2 The Geneious Prime Main Window 21 2.1 The Sources Panel.................................... 22 2.2 The Document Table .................................. 22 2.3 The Document Viewer Panel.............................. 25 2.4 The Toolbar ....................................... 26 2.5 The Help Panel ..................................... 27 2.6 Geneious Prime menu bar options .......................... 29 3 Importing and Exporting Data 35 3.1 Importing data from the hard drive to your Local folders............. 35 3.2 Data input formats ................................... 36 3.3 Importing files from public databases ........................ 44 3.4 Agents .......................................... 47 3.5 Exporting files...................................... 50 3.6 Printing and Saving Images.............................. 52 4 Managing Your Local Documents 55 4.1 Organizing your local documents........................... 55 4.2 Searching and filtering local documents....................... 58 4.3 Find Duplicates..................................... 62 4.4 Batch Rename...................................... 63 4.5 Backing up your local documents........................... 63 4.6 Document History ................................... 65 5 Creating, Viewing and Editing Sequences 67 5.1 Creating new sequences ................................ 67 5.2 The Sequence Viewer.................................. 69 5.3 Customizable text view for sequences ........................ 81 2 CONTENTS 3 5.4 Editing sequences.................................... 82 5.5 Complement and Reverse Complement ....................... 84 5.6 Translating sequences.................................. 85 5.7 Viewing chromatograms................................ 86 5.8 Meta-data ........................................ 88 6 Parent / Descendant Tracking 93 6.1 Editing Linked Documents............................... 94 6.2 The Lineage View.................................... 96 7 RNA, DNA and Protein Structure Viewer 99 7.1 RNA/DNA secondary structure fold viewer .................... 99 7.2 3D protein structure viewer ..............................100 8 Working with Annotations 103 8.1 Viewing, editing and extracting annotations.....................103 8.2 Adding annotations...................................108 8.3 Compare Annotations .................................113 9 Sequence Alignments 117 9.1 Dotplots .........................................117 9.2 Sequence Alignments..................................119 9.3 Alignment viewing and editing............................127 9.4 Alignment masking...................................130 9.5 Consensus sequences..................................132 10 Assembly and Mapping 135 10.1 Supported sequencing platforms ...........................135 10.2 Read processing.....................................136 10.3 De novo assembly....................................145 10.4 Map to reference.....................................149 10.5 The Contig Viewer ...................................155 10.6 Editing Contigs .....................................159 10.7 Extracting the Consensus................................160 11 Analysis of Assemblies and Alignments 161 11.1 Finding polymorphisms ................................161 11.2 Analyzing Expression Levels .............................164 12 Building Phylogenetic Trees 177 12.1 Phylogenetic tree representation ...........................177 12.2 Tree building in Geneious Prime ...........................178 12.3 Tree building methods and models..........................181 12.4 Resampling – Bootstrapping and jackknifing ....................183 12.5 Viewing and formatting trees .............................185 4 CONTENTS 13 Primers 189 13.1 Design New Primers ..................................189 13.2 Manual primer design .................................197 13.3 Importing primers from a spreadsheet........................199 13.4 Primer Database.....................................201 13.5 Test with Saved Primers ................................201 13.6 Add Primers to Sequence................................203 13.7 Characteristics for Selection ..............................204 13.8 Convert to Oligo.....................................204 13.9 Primer Extensions....................................204 13.10 Extract PCR Product ..................................206 13.11 More Information....................................206 14 Cloning 207 14.1 Find Restriction Sites..................................207 14.2 Digest into fragments..................................210 14.3 Creating a custom enzyme set.............................213 14.4 Introduction to the cloning interface .........................214 14.5 Restriction Cloning...................................216 14.6 Golden Gate.......................................217 14.7 Gibson Assembly....................................219 14.8 Gateway® Cloning ...................................221 14.9 TOPO® Cloning.....................................222 14.10 Copy-paste cloning...................................223 14.11 CRISPR site finder....................................223 14.12 Analyze Silent Mutations................................226 14.13 Optimize Codons....................................227 15 BLAST 231 15.1 Setting up a BLAST search...............................231 15.2 BLAST results......................................233 15.3 NCBI BLAST.......................................235 15.4 Adding alternative BLAST server locations .....................237 15.5 Custom BLAST .....................................237 16 Workflows 241 16.1 Managing Workflows..................................241 16.2 Creating and editing Workflows............................242 16.3 Custom code in Workflows ..............................246 17 Geneious Education 247 17.1 Creating a tutorial....................................247 17.2 Answering a tutorial ..................................248 18 Saving Operation Settings (Option Profiles) 249 CONTENTS 5 19 Shared Databases 251 19.1 Using a Shared Database................................251 19.2 Direct SQL Connection.................................255 19.3 Geneious Server Database...............................263 20 Advanced Administration 271 20.1 Default data location ..................................271 20.2 Change default preferences ..............................272 20.3 Pre-configuring Shared Database connections....................273 20.4 Pre-configuring license server location........................273 20.5 Adding custom plugins to the Plugins menu in Geneious Prime . 273 20.6 Deleting built-in plugins................................274 20.7 Max memory.......................................274 20.8 Web Linking to Data in Geneious Prime.......................275 6 CONTENTS Chapter 1 Getting Started The best way to get started with Geneious Prime is to try out some of our tutorials. The Tutorial option under the Help menu provides an inbuilt tutorial with a basic introduction to the major features of Geneious Prime. Additional tutorials on specialized functions can be downloaded from our website https://www.geneious.com/tutorials. For additional information and help with troubleshooting, please visit the Geneious support website at https://support.geneious.com. 1.1 Downloading & Installing Geneious Prime Geneious Prime is free to download from https://www.geneious.com/download. If you are a first-time user you will be offered a free trial. If you have already purchased a license you can enter it when Geneious Prime starts up. To download the latest version of Geneious Prime, click on https://www.geneious.com/ download (or type it in to your internet browser), choose the version you want to download and click Download. Geneious Prime can be run on Windows, Mac, or Linux. The following OS versions are sup- ported: Operating System Version Windows 7/8/10 Mac OS 10.8 - 10.15 Linux CentOS or RHEL 6 or higher/Ubuntu Desktop LTS, last 2 supported versions Note: From Geneious Prime 2020 onwards, only 64-bit Windows operating systems are sup- 7 8 CHAPTER 1. GETTING STARTED ported. We recommend at least the following specifications for running Geneious Prime (note that these are minimum requirements - for working with large datasets such as NGS sequences you will need a higher-spec machine): • Processor: Intel x86/x86 64 • Memory: 2048MB or more • Hard-disk: 2GB or more free space • Video: 1024x768 resolution or higher Geneious Prime comes bundled with the correct version of Java for your OS. If you require a version that does not include Java, please contact Geneious Support. Installing on Windows Download the installer for Windows, then double-click on it to run it and follow the prompts. The default installation location is in Program Files. Installing on macOS Download the installer for macOS. If the disk image does not automatically open, double-click on it to open it. Drag the Geneious icon to Applications to complete the installation. Installing on Linux The installer for linux is an executable script. To install Geneious Prime, open the Terminal and use the “cd” command to navigate to the location where you downloaded
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