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

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If you select the Contig Chromatogram section you can specify how many columns of traces you want to view at once, whether Sequencher should scroll to the selected column when you make a new selection in the contig and where the window should appear. Note: If you hold down the Ctrl key while changing the scale, the new scale will apply to all the traces in that window. If you hold down the Ctrl key while clicking any of the buttons to hide a lane, the lane(s) will be hidden for all the traces in the window. (See Figure 15-2 above.) Display secondary peak You can identify heterozygotes by identifying the second-highest peak beneath the primary peak. If you have a particular candidate for a heterozygote, first open the chromatogram for the individual sequence then click on the base call(s) as shown in Figure 15-3. Figure 15-3 Trace with base selected Go to the Sequence menu and choose Call Secondary Peaks…. A dialog box lets you specify how the secondary peak should be called (Figure 15-4). Figure 15-4 Secondary peak parameters The slider lets you specify how significant the second-highest peak must be to generate a change. In Figure 15-4 above, the slider is set so the secondary peak has to be at least 75% as high as the highest peak. If you want Ns to be replaced then select the Allow Ns to be replaced checkbox. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 140
If you’ve already edited bases by hand and don’t want them changed, you must deselect the checkbox called Allow edited bases to be replaced. If you select Only make changes that result in an ambiguity, Sequencher may change an ambiguous base call to an A, C, G or T if it does not meet the secondary peak criteria. If you prefer it to remain ambiguous do not select this option. If you wish to search just a range of bases, highlight them and check the Search Selection Only checkbox. When you click OK to make the changes, a dialog box notes how many bases will be changed; you can choose to Cancel or Continue at that point. If you continue, the changes take effect. Once they have taken effect, unlike normal edits to a base, they cannot be undone. Once you have pressed the Continue button, you can find all the changes made during the session by selecting the first base in the sequence (you can click on it right on the chromatogram) and going to the Select menu and clicking on Next Edited Base. After you execute any Select Next command, Sequencher creates a shortcut for that command in the spacebar so you can continue to search for your edits, using the same function over and over by simply pressing the space bar. Figure 15-5 Base change generated by secondary peak Select Next Commands The Select menu provides you with several commands for navigating to bases which need further review or attention (see Table 15-1). As you move your selection from each position that requires scrutiny to the next, you are likely to need to repeat these commands frequently. Therefore, Sequencher creates a shortcut for that command in the space bar after the first time you invoke a Next command. Press the space bar to move from one selected base to the next candidate. To change any Next command to search in the reverse direction, combine the command with the Shift key. If you use the Next Met To Stop (>0bp) you can highlight the next pair of start and stop codons in one of the three forward reading frames. The number of bases shown in this command depends on whether you specified a preference for a minimum length in the User Preferences. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 141
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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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Page 108 and 109: consensus is from a base with a low
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 116 and 117: Page Intentionally Left Blank SEQUE
Page 118 and 119: The Translated Variance Table If yo
Page 120 and 121: Structure of the Translated Varianc
Page 122 and 123: (see Figure 13-5). It is possible f
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 154 and 155: Note: Remember that even if a seque
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
Page 168 and 169: display this view by going to the V
Page 170 and 171: The default setting shows exact mat
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
Page 182 and 183: a dialog box (Figure 18-6). This le
Page 186 and 187: Figure 19-1 Export Options dialog b
Page 188 and 189: You should remember to provide a re
Page 190 and 191: Figure 19-3 Copy As Protein Transla
Page 192 and 193: [Project Name] and [User Name]. You
Page 196 and 197: Colors as Backgrounds Sometimes, di
Page 198 and 199: Choosing a genetic code You will fi
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Page 202 and 203: Label & Name The Label & Name prefe
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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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