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Download Information from Nine Important NCBI Databases and Perform NCBI BLAST Searches (Table 3.1)

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Download Information from Nine Important NCBI Databases and Perform NCBI BLAST Searches (Table 3.1) Geneious 8.1 Biomatters Ltd September 27, 2016 2 Contents 1 Getting Started5 1.1 Downloading & Installing Geneious..........................5 1.2 Geneious setup......................................6 1.3 Upgrading to new versions............................... 14 1.4 Licensing.......................................... 14 1.5 Troubleshooting...................................... 16 2 The Geneious main window 17 2.1 The Sources Panel..................................... 18 2.2 The Document Table................................... 18 2.3 The Document Viewer Panel............................... 20 2.4 The Help Panel...................................... 21 2.5 The Toolbar........................................ 22 2.6 The Menu Bar....................................... 23 3 Importing and Exporting Data 29 3.1 Importing data from the hard drive to your Local folders.............. 29 3.2 Data input formats.................................... 30 3.3 Importing files from public databases......................... 37 3.4 Agents........................................... 40 3.5 Exporting files....................................... 44 3 4 CONTENTS 3.6 Printing and Saving Images............................... 45 4 Managing your Local Documents 47 4.1 Organizing your local documents............................ 47 4.2 Searching and filtering local documents........................ 49 4.3 Find Duplicates...................................... 53 4.4 Batch Rename....................................... 54 4.5 Backing up your local documents............................ 54 4.6 Document History.................................... 56 5 Creating, viewing and editing sequences 57 5.1 Creating new sequences................................. 57 5.2 The Sequence Viewer................................... 58 5.3 Editing sequences..................................... 70 5.4 Complement and Reverse Complement........................ 72 5.5 Translating sequences................................... 72 5.6 Viewing chromatograms................................. 74 5.7 Meta-data......................................... 76 6 Parent / Descendant tracking 81 6.1 Editing Linked Documents............................... 83 6.2 The Lineage View..................................... 84 7 RNA, DNA and Protein structure viewer 87 7.1 RNA/DNA secondary structure fold viewer..................... 87 7.2 3D protein structure viewer............................... 88 8 Working with Annotations 91 8.1 Viewing, editing and extracting annotations...................... 91 8.2 Adding annotations.................................... 97 CONTENTS 5 8.3 Compare Annotations.................................. 100 9 Sequence alignments 105 9.1 Dotplots.......................................... 105 9.2 Sequence Alignments................................... 107 9.3 Alignment viewing and editing............................. 114 9.4 Consensus sequences................................... 118 10 Assembly and Mapping 121 10.1 De novo assembly..................................... 121 10.2 Map to reference...................................... 125 10.3 Trim Ends......................................... 126 10.4 Using paired reads.................................... 129 10.5 Splitting multiplex/barcode data............................ 130 10.6 Viewing Contigs...................................... 130 10.7 Editing Contigs...................................... 132 10.8 Saving the Consensus................................... 133 11 Analysis of assemblies and alignments 135 11.1 Finding polymorphisms................................. 135 11.2 Analyzing Expression Levels.............................. 138 12 Building Phylogenetic trees 143 12.1 Phylogenetic tree representation............................ 143 12.2 Tree building in Geneious................................ 144 12.3 Tree building methods and models........................... 145 12.4 Resampling – Bootstrapping and jackknifing..................... 147 12.5 Viewing and formatting trees.............................. 149 13 PCR Primers 153 6 CONTENTS 13.1 Design New Primers................................... 153 13.2 Manual primer design.................................. 159 13.3 Importing primers from a spreadsheet......................... 160 13.4 Primer Database...................................... 162 13.5 Test with Saved Primers................................. 163 13.6 Characteristics for Selection............................... 164 13.7 Convert to Oligo...................................... 164 13.8 Primer Extensions..................................... 165 13.9 Extract PCR Product................................... 165 13.10More Information..................................... 167 14 Cloning 169 14.1 Find Restriction Sites................................... 170 14.2 Digest into fragments................................... 171 14.3 Restriction Cloning.................................... 174 14.4 Gateway® Cloning.................................... 177 14.5 Gibson Assembly..................................... 177 14.6 TOPO® Cloning...................................... 180 14.7 CRISPR site finder.................................... 181 14.8 Optimize Codons..................................... 183 15 BLAST 187 15.1 Setting up a BLAST search................................ 187 15.2 BLAST results....................................... 189 15.3 NCBI BLAST........................................ 191 15.4 Custom BLAST...................................... 192 16 Saving operation settings (option profiles) 197 CONTENTS 7 17 Workflows 199 18 Geneious Education 201 18.1 Creating a tutorial..................................... 201 18.2 Answering a tutorial................................... 202 19 Collaboration 203 19.1 Managing Your Accounts................................ 204 19.2 Managing Your Contacts................................. 206 19.3 Sharing Documents.................................... 208 19.4 Browsing, Searching and Viewing Shared Documents................ 208 19.5 Chat............................................. 209 20 Shared Databases 211 20.1 Supported Database Systems.............................. 211 20.2 Setting up......................................... 212 20.3 Removing a Shared Database.............................. 213 20.4 Administration...................................... 213 21 Geneious Server 215 21.1 Introduction to Geneious Server............................. 215 21.2 Accessing Geneious Server................................ 215 21.3 Running jobs and retrieving results........................... 217 21.4 Geneious Server enabled plugins............................ 219 22 Advanced Administration 221 22.1 Default data location................................... 221 22.2 Change default preferences............................... 221 22.3 Specify license server location.............................. 222 22.4 Deleting plugins...................................... 222 8 CONTENTS 22.5 Max memory....................................... 223 22.6 Web Linking to Data in Geneious............................ 223 Chapter 1 Getting Started The best way to get started with Geneious is to try out some of our tutorials. The ”Tutorial” option under the Help menu in Geneious provides an inbuilt tutorial with a basic introduc- tion to the major features of Geneious. Additional tutorials on specialized functions can be downloaded from our website http://geneious.com/tutorials. For additional information and help with troubleshooting, please visit the Geneious support website at http://support.geneious.com. 1.1 Downloading & Installing Geneious Geneious is free to download from http://geneious.com/download. If you are using Geneious for the first time you will be offered a free trial. If you have already purchased a license you can enter it when Geneious starts up. To download the latest version of Geneious, click on http://geneious.com/download (or type it in to your internet browser), choose the version of Geneious you want to download and click Download. If you have a 64-bit Linux or Windows machine, ensure you check the ”64-bit” box. Geneious is compatible with the three most common operating systems: Windows, Mac, and Linux. Check that you have one of the following OS versions before you launch Geneious: Operating System System requirements Windows XP/Vista/7/8 Mac OS 10.6/10.7/10.8/10.9 Linux CentOS 6/RHEL6/Ubuntu Desktop LTS 9 10 CHAPTER 1. GETTING STARTED We recommend at least the following specifications for running Geneious (note that these are minimum requirements - for working with large datasets such NGS sequences you will need a higher-spec machine): • Processor: Intel x86/x86 64 • Memory: 2048 MB or more • Hard-disk: 2GB or more free space • Video: 1024x768 resolution or higher Geneious also needs Java 1.6 or higher to run. Geneious comes bundled with the correct version of Java for your OS. If you require a version of Geneious that does not include Java, please contact Geneious Support. Once Geneious has downloaded, double left-click on the Geneious icon to start installing the program. While this is happening, you will be prompted for a location to install Geneious. Please check that you are satisfied with the location before continuing. If you are using Mac OS X you will only have to double click on the disk image that is down- loaded then drag the Geneious application to your Applications folder. Don’t run Geneious from the mounted disk image as there are no write permissions on this. You must drag the icon into your Applications
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