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

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Viewing summary information in the Sequence Editor You can bring up summary information on your data from the Sequence Editor. Go to the File menu and choose Get Info…. The Get Info… window (in Figure 8-5) provides summary information on the sequence you are currently editing. Figure 8-5 Sequence information window If you want to annotate your data with more information than the comment box allows you to see, go to the Edit menu and click on Edit Comments… Sequencher will open a small text editing window that stores about 250 characters of text with each sequence. After you have added text with Edit Comments, a small “I” (for “Info”) will appear at the upper left corner of the icon. Base counts are displayed at the bottom of the window. If your sequence also includes confidence scores you will also see a base count for each of the three confidence ranges. If you use an ABI sequencing system click the Show ABI Info button. Sequencher displays a window with information from the ABI data sheet, shown in Figure 8-6. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 54
Figure 8-6 ABI data sheet info Selecting Bases Sequencher offers a number of ways to select bases. You can choose commands from the Select menu or you can use a keyboard combination. To select bases in the opposite orientation, press and hold the Shift key when using any Select Next… command (from the menu or with a keyboard shortcut). Finding Ambiguous Bases One of the most frequently executed commands is Next Ambiguous Base under the Select menu. You can use this command in the Sequence Editor or the contig editor. By using this command in the consensus sequence of a contig, Sequencher will display the next position in your contig that contains an ambiguity or disagreement. The shortcut for this command is Ctrl+N (for more on keyboard shortcuts see Appendix 23 “Keyboard shortcuts”). If you use the Shift key with this key combination, you will go back to the previous disagreement. Once you have used any of the Select Next commands, Sequencher will activate the space bar to execute that operation. If you use either the menu command or the shortcut key combination two consecutive times, Sequencher will remind you that this easier alternative is available. Finding Open Reading Frames (ORF) Choose Next Met to Stop (>0b) to 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. (For instructions on how to set a specified minimum length for open reading frames see Chapter 21 “Customizing Sequencher and User Preferences”.) If you set preferences to highlight ORFs only when they are of some minimum length, the menu command will display the number of bases you specified. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 55
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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
Page 20 and 21: Navigating Sequencher Help The Sequ
Page 22 and 23: Contig menu The commands in the Con
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Page 26 and 27: Figure 3-1 An empty Sequencher Proj
Page 28 and 29: Figure 3-4 Project Window with Larg
Page 30 and 31: value in the Confidence pane of the
Page 32 and 33: Editing the information for a seque
Page 36 and 37: How to import using menu commands I
Page 38 and 39: Figure 4-2 Browse for Folder dialog
Page 40 and 41: Importing Confidence Scores Many ba
Page 42 and 43: If you have finished working with S
Page 44 and 45: Selecting sequences Selecting seque
Page 46 and 47: Renaming a sequence or contig Renam
Page 48 and 49: Closing the Project Window When you
Page 50 and 51: Performing a trim with default sett
Page 52 and 53: additional control within the Trim
Page 54 and 55: Figure 6-7 The polylinker window No
Page 56 and 57: Setting Vector Trimming Criteria Se
Page 60 and 61: Basic Reference Sequence properties
Page 62 and 63: When the To Reference by Name comma
Page 66 and 67: A locked editor is read-only. You c
Page 68 and 69: If your sequence was called “MyPU
Page 72 and 73: Figure 8-7 ORF selected by Next Met
Page 74 and 75: If you want to assign a personal an
Page 76 and 77: Voice verification Sequencher provi
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
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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
Page 106 and 107: Consensus to Forensic Standards In
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 118 and 119: 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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Enabling the protein display To ena
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Note: Remember that even if a seque
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If you select the Contig Chromatogr
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Select command Table 15-1 Summary o
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Note: The Extend Selection command
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Figure 16-2 Restriction map options
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example, if you were displaying onl
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Figure 16-8 Checkmarked enzyme list
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display this view by going to the V
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The default setting shows exact mat
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Creating and editing features To cr
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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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