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

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Figure 13-13 Creating a Joined feature Setting the Variance Table Display Options Throughout Sequencher, you can customize the display of your sequences using the commands from the View menu. When creating a Variance Table, you can also specify a number of display options (see Table 13-1). Table 13-1 View Options Base Ambiguities Variance Table consensus Variance Table Translated Variance Table No No No No Translated consensus Variance Table Base Edits Yes No No No Display Color Bases Display Features Yes Yes No No Yes Yes No No Display Motifs No No No No Colors As Backgrounds Yes Yes No No Display Base Confidences Yes No No No Labels Yes Yes Yes Yes To highlight variants in your data, go to the View menu and click on Display Base Confidences. This will add a background color to the cells in your Variance Table to SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 112
indicate that there is an associated confidence or quality score range for the variant. Variants that require additional checking because they have a low confidence or quality score will be highlighted with dark blue. Those with medium or high confidence scores will be highlighted with a medium or pale blue background. If you click on Display Color Bases and Display Colors as Backgrounds it can help you to see patterns in your data (see Figure 13-14). You can use Base Ambiguities As to distinguish ambiguous or edited bases. You can also toggle the display of features from the View menu. You can use the Label command to mark sequences in the table. Set your preferences using the Label & Name preferences pane. Use the boxes grouped under Available Labels in the preference pane to choose label colors and descriptions for marking individual sequences. Select the sequence you want to label by clicking its column header. Go to the Edit menu and choose the Label submenu. The display name of the sequence will change to match the color of the Label. (See Figure 13-14.) Notice how the tool tip provides the name of the sample, its label and other attributes. (Refer to Chapter 21 “Customizing Sequencher and User Preferences” for more detailed information.) Figure 13-14 The Variance Table Display Options Setting the Consensus Calculation for a Variance Table You can generate a Variance Table where the exemplar is a consensus sequence rather then the Reference Sequence by using the Compare Bases To command from the Sequence menu. You generate a consensus Variance Table using the Compare Consensus to Reference command from the Contig menu. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 113
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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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Page 80 and 81: Chapter 9 “Sequence Assembly” f
Page 82 and 83: Figure 9-2 The Clean Data algorithm
Page 84 and 85: Performing the assembly Automatic a
Page 86 and 87: Figure 9-5 Interactive assembly sho
Page 88 and 89: The new contig will appear in the P
Page 90 and 91: When you use a Name Delimiter, it w
Page 92 and 93: If the Expression is a delimiter bo
Page 94 and 95: Figure 10-6 The Project Window with
Page 98 and 99: it is in the reverse orientation. T
Page 100 and 101: Figure 11-2 Contig overview Fifure
Page 102 and 103: Base Numbers At Transitions Clickin
Page 104 and 105: Label Name Function E F G H Sequenc
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Page 110 and 111: move the gaps to the 5’ end, sele
Page 112 and 113: Figure 12-4 Fill Void dialog box De
Page 114 and 115: First select the base or range of b
Page 118 and 119: The Translated Variance Table If yo
Page 120 and 121: Structure of the Translated Varianc
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Page 124 and 125: Figure 13-7 Translated Variance Tab
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Page 130 and 131: In either case, the method you choo
Page 132 and 133: You can edit your data directly in
Page 134 and 135: Figure 13-17 The Translated Varianc
Page 136 and 137: Figure 13-19 Extract from Variance
Page 138 and 139: The Population Table lists the vari
Page 140 and 141: If you want to remove sample sequen
Page 142 and 143: Select Individual Variance Reports
Page 144 and 145: If you prefer to copy your Translat
Page 146 and 147: You can copy your Translated Varian
Page 148 and 149: Summary report display options Sequ
Page 150 and 151: Enabling the protein display To ena
Page 154 and 155: Note: Remember that even if a seque
Page 156 and 157: If you select the Contig Chromatogr
Page 158 and 159: Select command Table 15-1 Summary o
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
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Figure 18-1 A dimmed icon Finding t
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Note: If you pause between characte
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a dialog box (Figure 18-6). This le
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Figure 19-1 Export Options dialog b
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You should remember to provide a re
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Figure 19-3 Copy As Protein Transla
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[Project Name] and [User Name]. You
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Colors as Backgrounds Sometimes, di
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Choosing a genetic code You will fi
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time you select the Review button f
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Label & Name The Label & Name prefe
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Click the Use Blank Project radio b
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Use the Columns For Multiple Traces
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If you are making changes to the wa
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Variance Table The Variance Table p
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Figure 22-1 The Validate mtDNA Prof
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Figure 22-3 The Circular Genome Siz
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Menu/Window Command Windows Select
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You may require a more complex deli
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Code Base(s) Meaning 5 A or Another
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Feature Display Color Style Second
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eferences numbers, sequences, or us
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Qualifier type Description Citation
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Feature Key Default Feature Qualifi
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Name CursorProject Window Dialog bo
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