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

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Note: Remember that even if a sequence fragment is incorporated into a contig, you can still open its editor by double-clicking the sequence name in the list at the left of the contig editor. Viewing chromatograms from a contig editor The Sequencher contig editor allows you to view simultaneously all chromatogram data relevant to a consensus base call. If you are at the 5’ end of the contig, Sequencher selects the most 5’ base in the consensus and displays all the associated traces. If you are elsewhere in the contig, Sequencher selects the center-most consensus base in the contig display and displays the associated traces. This allows you to check the signal strength of any peak in conjunction with its base call and edit your data accordingly. Select a contig column by clicking on its base in the consensus line (Figure 15-1). Then click the Show Chromatogram button or go to the Window menu and choose Chromatogram. Sequencher opens a window to display the traces (Figure 15-1). The bases you highlighted in the contig editor will also be highlighted in the trace windows. Figure 15-1 Selected column chromatograms SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 138
When you click the Show Chromatograms button in a region without trace data you will see a “No Chromatogram Data” message in the Contig Chromatogram window. When you move the cursor back into a region where there are fragments with chromatogram data, the traces will reappear. Understanding the Trace Display Above the traces are two lines of bases. The upper line displays the sequence as it currently appears in the editor, including any edits you may have made. The lower line displays the base calls as originally imported, including the trimmed data. The arrows to the left show the orientation and relative lengths of the trimmed and untrimmed data. Below the arrows is a slider for changing the height of the trace. Below the slider are four buttons that let you hide the lanes for any or all of the traces. Click on the button to hide any lane. Click it again to display the lane. Figure 15-2 shows a contig with adjusted scales and hidden lanes. Scrolling through a single chromatogram is simple. Position your cursor on the small rectangular slider button to the right of the trace. With the mouse button held down, you can move the slider down or up, depending on your current position within the sequence. Alternately, you can use the left arrow and right arrow keys to step through the sequence trace, base by base. When you are working in a contig, if you highlight a base in the consensus line you can use the arrow keys to move through the consensus sequence. Note that as you do so all the contig chromatograms will move left or right, in step with the highlighted base. Figure 15-2 Trace with hidden lanes and adjusted scales You can specify the settings for trace display by going to the Window menu and choosing User Preferences and selecting Chromatogram. You can specify the height of the trace, the width from peak to peak, the way the lanes are identified and various screen display attributes. (See Chapter 21 on “Customizing Sequencher and User Preferences” for more information.) SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 139
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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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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
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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
Page 126 and 127: If you want to restrict the Compari
Page 128 and 129: Figure 13-13 Creating a Joined feat
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 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
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
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Page 198 and 199: Choosing a genetic code You will fi
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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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