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

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Colors as Backgrounds Sometimes, displaying bases in color does not differentiate them enough. You can further enhance the colored bases by going to the View menu and choosing Colors As Backgrounds. Sequencher then displays the base as a colored rectangle with the base character printed over it. Display Base Confidences Sequencher can represent imported confidence scores as a colored background. In order to view base confidence values as colored backgrounds, go to the View menu and click on Display Base Confidences. Sequencher will only display these backgrounds if the original data included base quality scores. (For information on how to change the threshold values see the section “User Preferences” in this chapter.) You may need to turn off Colors As Backgrounds. Display Features Sequencher can display features you have entered. Go to the View menu and click on Display Features to toggle this view on and off. For each individual feature you must also enable or disable its display in User Preferences. (See also Chapter 17, “Motifs and Features” for more information.) Display Motifs Sequencher can display motifs you have entered. Go to the View menu and click on Display Motifs to toggle this view on and off. (See Chapter 17, “Motifs and Features” for more information.) Setting up custom codes Standard coding system The IUPAC-IUB ambiguity set is the most common coding system for representing DNA. Some commercial and academic software packages also use the Stanford Extended System codes, which include one-character representations for “maybe A,” “probably G,” etc. Sequencher defaults to the IUPAC-IUB system, but includes a copy of the Stanford extended set. See Appendix 25 and Appendix 26 for tables of the IUPAC-IUB and Stanford Extended code systems. Configuring Ambiguity Codes If you wish to configure Sequencher’s ambiguity coding system yourself, go to the Window menu and choose Ambiguity/Key Codes... Sequencher displays the dialog box shown in Figure 21-1. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 180
Figure 21-1 Ambiguity editor Each base and each ambiguity has a display character which is drawn on the screen and sent to the printer to represent that base or ambiguity. The display character interprets ASCII text files imported into Sequencher. Each code is also assigned a color which can be displayed in fragments or contigs by going to the View menu and clicking on Display Color Bases. Select a base or ambiguity from the scrolling list at the left by clicking on its name. When the item is highlighted, information about it appears on the right side of the dialog box. To change the display character, click the box to highlight it. Replacing an existing character keystroke code Each base code can be assigned up to two alternate keys from the keyboard. Using either of these keys generates the desired base code when using the sequence or contig editors. These keystroke settings do not affect importing of data. To change a keystroke setting for a base code, select the base code from the list on the left of the window. Click on one of the keyboard keys to highlight it and then press the key you want to assign to that base code. To change a color setting for a base code, select the base code from the list on the left of the window. Select a different color from the Color drop down menu. Saving and loading custom codes You can load and save your customized ambiguity settings by going to the button bar at the top of the Ambiguity Editor and clicking on Load Ambiguities and then Save Ambiguities. Show and hide ambiguity helper Sequencher can show a small quick-reference window that lists the current ambiguity symbols. To bring up this window, go to the Window menu and click on Show Ambiguity Helper. Close the window with the close box in the upper right corner. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 181
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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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Page Intentionally Left Blank SEQUE
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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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Page 148 and 149: Summary report display options Sequ
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Page 154 and 155: Note: Remember that even if a seque
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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 190 and 191: Figure 19-3 Copy As Protein Transla
Page 192 and 193: [Project Name] and [User Name]. You
Page 198 and 199: Choosing a genetic code You will fi
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Page 204 and 205: Click the Use Blank Project radio b
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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
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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
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Page 234 and 235: Qualifier type Description Citation
Page 236 and 237: Feature Key Default Feature Qualifi
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