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

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time you select the Review button from the Variance Table, Sequencher will open the windows in your layout positions. User Preferences You can specify your preferences for many program settings in Sequencher. To set these, go to the Window menu and choose User Preferences…. The User Preferences window contains a hierarchical list of preference settings. The main categories of settings are General, Display and Input/Output. Click the triangle sign next to a category name to expand the list and show the various preference topics within that category. When a category list is expanded the triangle changes to point downwards. When you click a preference topic name, a Preference Pane appears on the right side of the window and enables you to specify your preferences for that topic. Note: Each preference setting you select will be stored when you quit the program. General Settings In the File menu you will find a command called Open Recent. The submenu for this command is a list of projects. You can specify the number of recent projects Sequencher will remember in this submenu. The maximum number is 99. Sequencher is installed with a set of default values. As you work with the program, it replaces the default values with your preferences. However, if you want to restore the original settings, you will find a button at the bottom of the Settings user preferences called Reset user preferences to factory defaults. This option resets all of the user preferences to their original status. Auto-Save Auto-Save preferences control the timing of automatic saving of project files. To use this preference, you must have saved your data and given your project a name at least once. To activate Auto-Save, click the Auto-Save Project Files checkbox. Click the Ask Before Each Auto-Save checkbox if you want to confirm the save each time. Use the Time Between Saves slider to set how long Sequencher should wait between each Auto-Save. Use the Idle Time Before Auto-Save slider to set how long your computer should be idle before Sequencher executes an Auto-Save. The latter setting will prevent Sequencher from performing an Auto-Save while you are typing. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 184
Figure 21-5 Auto Save preference settings Confidence Many of the new base callers generate confidence values associated with each base. Sequencher supports confidence values from PHRED, ACE, Trace Tuner, SCF, ABI, ESD and compatible files. The Confidence preferences control the display of base calls and confidence values from these files. Sequencher’s default settings show confidences below 20 as dark blue, the midrange values as a medium blue and high confidences, that is above 40, as a light blue. Change the threshold values by altering the numbers in either Confidence Ranges: box. Figure 21-6 Confidence Ranges: settings SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 185
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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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Page 154 and 155: Note: Remember that even if a seque
Page 156 and 157: If you select the Contig Chromatogr
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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
Page 168 and 169: display this view by going to the V
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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
Page 180 and 181: Note: If you pause between characte
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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
Page 192 and 193: [Project Name] and [User Name]. You
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Page 198 and 199: Choosing a genetic code You will fi
Page 202 and 203: Label & Name The Label & Name prefe
Page 204 and 205: Click the Use Blank Project radio b
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
Page 240 and 241: Name CursorProject Window Dialog bo
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