Clc Sequence Viewer Qiagen Bioinformatics-Books Pdf

CLC Sequence Viewer QIAGEN Bioinformatics
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Manual for,CLC Sequence Viewer 8 0 0,Windows macOS and Linux. June 1 2018,This software is for research purposes only. QIAGEN Aarhus,Silkeborgvej 2,DK 8000 Aarhus C,I Introduction 7. 1 Introduction to CLC Sequence Viewer 8,1 1 Contact information 9. 1 2 Download and installation 9,1 3 System requirements 11.
1 4 When the program is installed Getting started 12. 1 5 Plugins 13,1 6 Network configuration 16,1 7 Latest improvements 16. II Core Functionalities 18,2 User interface 19,2 1 Navigation Area 20. 2 2 View Area 27,2 3 Zoom and selection in View Area 35. 2 4 Toolbox and Status Bar 37,2 5 Workspace 40,2 6 List of shortcuts 41. 3 User preferences and settings 44,3 1 General preferences 44.
3 2 View preferences 46,3 3 Advanced preferences 49. 3 4 Export import of preferences 49,CONTENTS 4,3 5 View settings for the Side Panel 50. 4 Printing 52,4 1 Selecting which part of the view to print 53. 4 2 Page setup 54,4 3 Print preview 56,5 Import export of data and graphics 57. 5 1 Standard import 57,5 2 Data export 59,5 3 Export graphics to files 68.
5 4 Export graph data points to a file 72,5 5 Copy paste view output 73. 6 Data download 75,6 1 Search for Sequences at NCBI 75. III Bioinformatics 78,7 Viewing and editing sequences 79. 7 1 View sequence 79,7 2 Circular DNA 85,7 3 Working with annotations 87. 7 4 Element information 93,7 5 View as text 94,7 6 Sequence Lists 95.
8 Viewing structures 98,8 1 Importing molecule structure files 99. 8 2 Viewing molecular structures in 3D 99,8 3 Customizing the visualization 100. 8 4 Tools for linking sequence and structure 109,9 General sequence analyses 111. 9 1 Extract sequences 111,CONTENTS 5,9 2 Shuffle sequence 113. 9 3 Sequence statistics 114,9 4 Join sequences 118.
10 Nucleotide analyses 120,10 1 Convert DNA to RNA 120. 10 2 Convert RNA to DNA 121,10 3 Reverse complements of sequences 121. 10 4 Reverse sequence 122,10 5 Translation of DNA or RNA to protein 123. 10 6 Find open reading frames 124,11 Restriction site analyses 127. 11 1 Dynamic restriction sites 127,11 2 Restriction Site Analysis 131.
11 3 Restriction enzyme lists 133,12 Sequence alignment 135. 12 1 Create an alignment 135,12 2 View alignments 140. 12 3 Edit alignments 142,13 Phylogenetic trees 146. 13 1 Create tree 147,13 2 Tree Settings 151,IV Appendix 159. A More features 160,B Graph preferences 161,C Formats for import and export 163.
C 1 List of bioinformatic data formats 163,C 2 List of graphics data formats 165. CONTENTS 6,D Restriction enzymes database configuration 167. E IUPAC codes for amino acids 168,F IUPAC codes for nucleotides 169. Bibliography 170,V Index 172,Introduction,Introduction to CLC Sequence Viewer. 1 1 Contact information 9,1 2 Download and installation 9.
1 2 1 Program download 9,1 2 2 Installation on Microsoft Windows 9. 1 2 3 Installation on macOS 10,1 2 4 Installation on Linux with an installer 11. 1 3 System requirements 11,1 3 1 CLC Sequence Viewer vs Workbenches 12. 1 4 When the program is installed Getting started 12. 1 4 1 Quick start 12,1 5 Plugins 13,1 5 1 Install 13. 1 5 2 Uninstall 14,1 5 3 Updating plugins 15,1 6 Network configuration 16.
1 7 Latest improvements 16, Welcome to CLC Sequence Viewer 8 0 0 a software package supporting your daily bioinformatics. We strongly encourage you to read this user manual in order to get the best possible basis for. working with the software package,This software is for research purposes only. CHAPTER 1 INTRODUCTION TO CLC SEQUENCE VIEWER 9,1 1 Contact information. The CLC Sequence Viewer is developed by,QIAGEN Aarhus. Silkeborgvej 2,8000 Aarhus C,http www qiagenbioinformatics com.
Email ts bioinformatics qiagen com, The QIAGEN Aarhus team is continuously improving the CLC Sequence Viewer with our users. interests in mind We welcome all requests and feedback from users as well as suggestions for. new features or more general improvements to the program. Users of the freely available CLC Sequence Viewer can make use of any of our online doc. umentation sources including the manuals http www qiagenbioinformatics com. support manuals tutorials http www qiagenbioinformatics com support tutorials. and other entries in our FAQ area http helpdesk clcbio com index php pg kb. 1 2 Download and installation, The CLC Sequence Viewer is developed for Windows macOS and Linux The software for either. platform can be downloaded from http www qiagenbioinformatics com product. 1 2 1 Program download, Before you download the program you are asked to fill in the Download dialog. In the dialog you must choose,Which operating system you use. Whether you would like to receive information about future releases. When the download of the installer an application which facilitates the installation of the. program is complete follow the platform specific instructions below to complete the installation. 1 2 2 Installation on Microsoft Windows, When you have downloaded an installer locate the downloaded installer and double click the.
icon The default location for downloaded files is your desktop. Installing the program is done in the following steps. On the welcome screen click Next,CHAPTER 1 INTRODUCTION TO CLC SEQUENCE VIEWER 10. Read and accept the License agreement and click Next. Choose where you would like to install the application and click Next. Choose a name for the Start Menu folder used to launch CLC Sequence Viewer and click. Choose if CLC Sequence Viewer should be used to open CLC files and click Next. Choose where you would like to create shortcuts for launching CLC Sequence Viewer and. click Next, Choose if you would like to associate clc files to CLC Sequence Viewer If you check this. option double clicking a file with a clc extension will open the CLC Sequence Viewer. Wait for the installation process to complete choose whether you would like to launch CLC. Sequence Viewer right away and click Finish, When the installation is complete the program can be launched from the Start Menu or from one. of the shortcuts you chose to create,1 2 3 Installation on macOS. Starting the installation process is done in the following way When you have downloaded an. installer locate the downloaded installer and double click the icon The default location for. downloaded files is your desktop, Launch the installer by double clicking on the CLC Sequence Viewer icon.
Installing the program is done in the following steps. On the welcome screen click Next, Read and accept the License agreement and click Next. Choose where you would like to install the application and click Next. Choose if CLC Sequence Viewer should be used to open CLC files and click Next. Choose whether you would like to create desktop icon for launching CLC Sequence Viewer. and click Next, Choose if you would like to associate clc files to CLC Sequence Viewer If you check this. option double clicking a file with a clc extension will open the CLC Sequence Viewer. Wait for the installation process to complete choose whether you would like to launch CLC. Sequence Viewer right away and click Finish, When the installation is complete the program can be launched from your Applications folder or. from the desktop shortcut you chose to create If you like you can drag the application icon to. the dock for easy access,CHAPTER 1 INTRODUCTION TO CLC SEQUENCE VIEWER 11. 1 2 4 Installation on Linux with an installer, Navigate to the directory containing the installer and execute it This can be done by running a.
command similar to,sh CLCSequenceViewer 7 8 64 sh, Installing the program is done in the following steps. On the welcome screen click Next, Read and accept the License agreement and click Next. Choose where you would like to install the application and click Next. For a system wide installation you can choose for example opt or usr local If you do not. have root privileges you can choose to install in your home directory. Choose where you would like to create symbolic links to the program. DO NOT create symbolic links in the same location as the application. Symbolic links should be installed in a location which is included in your environment PATH. For a system wide installation you can choose for example usr local bin If you do not. have root privileges you can create a bin directory in your home directory and install. symbolic links there You can also choose not to create symbolic links. Wait for the installation process to complete and click Finish. If you choose to create symbolic links in a location which is included in your PATH the program. can be executed by running the command,clcseqview7. Otherwise you start the application by navigating to the location where you choose to install it. and running the command,clcseqview7,1 3 System requirements. The system requirements of CLC Sequence Viewer are these. Windows 7 Windows 8 Windows 10 Windows Server 2012 and Windows Server 2016. OS X 10 10 10 11 and macOS 10 12 10 13, Linux RHEL 6 7 and later SUSE Linux Enterprise Server 11 and later The software is.
expected to run without problem on other recent Linux systems but we do not guarantee. 1 GB RAM required,CHAPTER 1 INTRODUCTION TO CLC SEQUENCE VIEWER 12. 2 GB RAM recommended,1024 x 768 display required,1600 x 1200 display recommended. 1 3 1 CLC Sequence Viewer vs Workbenches, CLC Sequence Viewer is a free user friendly application offering access to basic bioinformatics. analyses It can also be used to view some of the analysis outputs of CLC commercial. workbenches with the exceptions of some more advanced data types such as track based data. and data stored on a CLC Genomics Server, The analysis and viewing functionalities of the CLC Sequence Viewer are also available by running. the CLC Genomics Workbench version 11 0 and higher in Viewing Mode Using the Viewing Mode. of CLC Genomics Workbench you can also view all data types supported by the CLC Genomics. Workbench such as tracks heat maps and PCA plots If you have access to a CLC Genomics. Server you can also connect to it and view data held on the server Viewing Mode does not. require a license and can be used for free See section for further details. Workflows and tools on commercial Workbenches can only be viewed using a commercial. Workbench with a valid license installed, CLC Workbenches including CLC Sequence Viewer are available for Windows Mac and Linux.
1 4 When the program is installed Getting started, CLC Sequence Viewer includes an extensive Help function which can be found in the Help menu. of the program s Menu bar or by pressing F1 The help topics are sorted in a table of contents. and the topics can be searched, Tutorials describing hands on examples of how to use the individual tools and features of. the CLC Sequence Viewer can be found at http www qiagenbioinformatics com. support tutorials We also recommend our Online presentations where a product. specialist demonstrates our software This is a very easy way to get started using the. program Read more about video tutorials and other online presentations here http tv. qiagenbioinformatics com,1 4 1 Quick start, When the program opens for the first time the background of the workspace is visible. In the background you can see quick start shortcuts which will help you getting started. These can be seen in figure 1 1, The function of the quick start shortcuts is explained here. Import data Opens the Import dialog which you let you browse for and import data from. your file system,CHAPTER 1 INTRODUCTION TO CLC SEQUENCE VIEWER 13.
Figure 1 1 Quick start short cuts available in the background of the workspace. New sequence Opens a dialog which allows you to enter your own sequence. Read tutorials Opens the tutorials menu with a number of tutorials These are also. available from the Help menu in the Menu bar, It might be easier to understand the logic of the program by trying to do simple operations on. existing data Therefore CLC Sequence Viewer includes includes an example data set available in. the Help menu of the program,1 5 Plugins, When you install CLC Sequence Viewer it has a standard set of features However you can. upgrade and customize the program using a variety of plugins. As the range of plugins is continuously updated and expanded they will not be listed here. Instead we refer to http www qiagenbioinformatics com plugins for a full list of. plugins with descriptions of their functionalities. Note In order to install plugins and modules the Workbench must be run in administrator mode. On Linux and Mac it means you must be logged in as an administrator On Windows you can do. this by right clicking the program shortcut and choosing Run as Administrator. Plugins are installed and uninstalled using the plugin manager. Help in the Menu Bar Plugins or Plugins in the Toolbar. The plugin manager has two tabs at the top, Manage Plugins This is an overview of plugins that are installed. Download Plugins This is an overview of available plugins on QIAGEN Aarhus server. 1 5 1 Install, To install a plugin click the Download Plugins tab This will display an overview of the plugins. that are available for download and installation see figure 1 2. Select the plugin of interest to display additional information about the plugin on the right side of. the dialog Click Download and Install to add the plugin functionalities to your workbench. Accepting the license agreement, Part of the installation involves checking and accepting the end user license agreement EULA.
as seen in figure 1 3,CHAPTER 1 INTRODUCTION TO CLC SEQUENCE VIEWER 14. Figure 1 2 The plugins that are available for download. Figure 1 3 Read the license agreement carefully, Please read the EULA text carefully before clicking in the box next to the text I accept these. terms to accept If requested fill in your personal information before clicking Finish. If the plugin is not shown on the server but you have the installer file on your computer for. example if you have downloaded it from our website you can install the plugin by clicking the. Install from File button at the bottom of the dialog and specifying the plugin cpa file saved on. your computer, When you close the dialog you will be asked whether you wish to restart the workbench The. plugin will not be ready for use until you have restarted. 1 5 2 Uninstall,Plugins are uninstalled using the plugin manager. CHAPTER 1 INTRODUCTION TO CLC SEQUENCE VIEWER 15, Help in the Menu Bar Plugins or Plugins in the Toolbar.
This will open the dialog shown in figure 1 4, Figure 1 4 The plugin manager with plugins installed. The installed plugins are shown in the Manage plugins tab of the plugin manager To uninstall. select the plugin in the list and click Uninstall, If you do not wish to completely uninstall the plugin but you do not want it to be used next time. you start the Workbench click the Disable button, When you close the dialog you will be asked whether you wish to restart the workbench The. plugin will not be uninstalled until the workbench is restarted. 1 5 3 Updating plugins, If a new version of a plugin is available you will get a notification during start up as shown in. figure 1 5,Figure 1 5 Plugin updates, In this list select which plugins you wish to update and click Install Updates If you press.
Cancel you will be able to install the plugins later by clicking Check for Updates in the Plugin.

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