Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

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Label & Name The Label & Name preferences control the labels and descriptions used to mark sequences and contigs. Use the boxes grouped under Available Labels to choose label colors (use the pull down color menus at the left of the label name) and descriptions for marking individual sequences. Once you have set your preferences here you can apply them to sequences, contigs and refrigerators while you are working in a project by selecting the icon(s) in the Project Window. Go to the Edit menu and choose the Label submenu. Under the Default Names section of the Label & Name pane, you can enter default names for the new contigs and fragments. A bracketed asterisk tells Sequencher to add a number to the name and increase it for each new contig or fragment you add to the project. Figure 21-7 Label and name preference settings Menu The Menu preferences control command options that let you optimize the way you work in your own lab. Use the buttons under Use Ctrl+O For to program the Ctrl+O key combination to open a project or open a window. Use the pull down menus grouped under User-Defined Command Keys to create keyboard shortcuts for any of the menu commands. After you have assigned a keyboard shortcut to a menu item, the shortcut will be listed to the right of the menu command on the drop down menus. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 186
Figure 21-8 Menu preference settings Sound Sequencher provides audio feedback to help you maintain the quality of data input. When you select the Sound icon, you will see the preference pane shown in Figure 21-9. The slider controls how quickly Sequencher reads bases to you. Click the Play Audible Welcome at Startup checkbox if you want Sequencher to say “hello” at startup. Figure 21-9 Sound preference settings Note: You have to select a voice file to get audio output. (For more details, see Chapter 8 “The Sequence Editor” and review the section on “Voice Verification.”) New Project This User Preference determines what type of project will be opened by the New Project command. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 187
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THIS IS AN AGREEMENT BETWEEN YOU, T
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© 1991 - 2007 Gene Codes Corporati
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Templates .........................
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Set Circular Genome Size ..........
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The Bases View ....................
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Protein translations for the Consen
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Setting header, footer and margin o
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We welcome your comments or support
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Navigating Sequencher Help The Sequ
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Contig menu The commands in the Con
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Figure 3-1 An empty Sequencher Proj
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Figure 3-4 Project Window with Larg
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value in the Confidence pane of the
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Editing the information for a seque
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How to import using menu commands I
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Figure 4-2 Browse for Folder dialog
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Importing Confidence Scores Many ba
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If you have finished working with S
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Selecting sequences Selecting seque
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Renaming a sequence or contig Renam
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Closing the Project Window When you
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Performing a trim with default sett
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additional control within the Trim
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Figure 6-7 The polylinker window No
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Setting Vector Trimming Criteria Se
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Basic Reference Sequence properties
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When the To Reference by Name comma
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A locked editor is read-only. You c
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If your sequence was called “MyPU
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Viewing summary information in the
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Figure 8-7 ORF selected by Next Met
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If you want to assign a personal an
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Voice verification Sequencher provi
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Chapter 9 “Sequence Assembly” f
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Figure 9-2 The Clean Data algorithm
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Performing the assembly Automatic a
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Figure 9-5 Interactive assembly sho
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The new contig will appear in the P
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When you use a Name Delimiter, it w
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If the Expression is a delimiter bo
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Figure 10-6 The Project Window with
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it is in the reverse orientation. T
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Figure 11-2 Contig overview Fifure
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Base Numbers At Transitions Clickin
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Label Name Function E F G H Sequenc
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Consensus to Forensic Standards In
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consensus is from a base with a low
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move the gaps to the 5’ end, sele
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Figure 12-4 Fill Void dialog box De
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First select the base or range of b
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The Translated Variance Table If yo
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Structure of the Translated Varianc
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(see Figure 13-5). It is possible f
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Figure 13-7 Translated Variance Tab
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If you want to restrict the Compari
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Figure 13-13 Creating a Joined feat
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In either case, the method you choo
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You can edit your data directly in
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Figure 13-17 The Translated Varianc
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Figure 13-19 Extract from Variance
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The Population Table lists the vari
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If you want to remove sample sequen
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Select Individual Variance Reports
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If you prefer to copy your Translat
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You can copy your Translated Varian
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Summary report display options Sequ
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Enabling the protein display To ena
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Page 160 and 161: Note: The Extend Selection command
Page 162 and 163: Figure 16-2 Restriction map options
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Page 166 and 167: Figure 16-8 Checkmarked enzyme list
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Page 172 and 173: Creating and editing features To cr
Page 174 and 175: Quick feature creation To create a
Page 178 and 179: Figure 18-1 A dimmed icon Finding t
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Page 186 and 187: Figure 19-1 Export Options dialog b
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Page 190 and 191: Figure 19-3 Copy As Protein Transla
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Page 198 and 199: Choosing a genetic code You will fi
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Page 206 and 207: Use the Columns For Multiple Traces
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Page 210 and 211: Variance Table The Variance Table p
Page 214 and 215: Figure 22-1 The Validate mtDNA Prof
Page 216 and 217: Figure 22-3 The Circular Genome Siz
Page 220 and 221: Menu/Window Command Windows Select
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Page 226 and 227: Code Base(s) Meaning 5 A or Another
Page 228 and 229: Feature Display Color Style Second
Page 232 and 233: eferences numbers, sequences, or us
Page 234 and 235: Qualifier type Description Citation
Page 236 and 237: Feature Key Default Feature Qualifi
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