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

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Base Numbers At Transitions Clicking Base Numbers at Transitions displays or hides the numbers showing approximate positions of the coverage transitions. Base Numbers At Every x Bases Selecting Base Numbers Every x Bases shows the base numbers at constant intervals. Condensed Base Numbers Selecting the Condensed Base Numbers option changes the font of the base numbers to a compressed version. This option can be used with either Base Numbers at Transitions or Base Numbers at Every x Bases. Getting more information Find You can search for a specific subsequence in your contig. Fragments, which contain the subsequence, will appear with a heavier line in the Overview. You can choose to find the first occurrence by clicking the Find button. You can search for subsequent occurrences using the Find Next button. Three radio buttons allow you to control the specificity of the search by choosing Exact Matches, Specified Bases (which would allow you to use ambiguity codes such as W to find T or A). You can use the Any Ambiguous Base command, which will find any degenerate DNA that may match. There is also a drop down menu from which you may choose restriction enzyme sequences. If you have used a Reference Sequence and want to include it in the search, select the Include Reference Sequence in Find checkbox Close the dialog box by pressing Done. Get Info Summary information about the open contig can be obtained by pressing the Get Info button or go to the File menu and click on the Get Info command. The Bases View Working in the Bases View To get from the Overview to the view used for editing a contig, click the Bases button. Alternatively, you can go to the View menu and then go to the Bases, Map, Overview… submenu and choose Bases. Sequencher displays the contig editing window shown in Figure 11-5. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 86
Figure 11-5 The contig editing window To return to the overview click the Overview button or go to the Bases, Map, Overview… submenu and choose Overview. The labels in Figure 11-6 identify the different parts of the contig editor. Figure 11-6 Identifying parts of the contig editor Label Name Function Table 11-1 Key to the Contig Editor A Button Bar Contains several buttons you click to perform frequently-used functions. B Sequence list Shows which sequences make up the contig you are editing. C Agent Describes current selection and the current status of the spacebar shortcut. D Splitter bar Controls the width of list/message area and the editing area; dragging the splitter bar to the left or right changes the size of these items. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 87
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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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Page 54 and 55: Figure 6-7 The polylinker window No
Page 56 and 57: Setting Vector Trimming Criteria Se
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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 70 and 71: Viewing summary information in the
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 104 and 105: 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 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 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
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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
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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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