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

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If you want to assign a personal annotation, select Sequencher from the drop down menu called Feature Key:. To give the feature a name, type your text into the Feature Name: box. You can use the default display style or you can assign a Feature Color and Feature Style, such as inverted case or underlined, from the dialog box. You can also use the Display: radio buttons to determine whether single stranded DNA is displayed or RNA, protein translation or the complement will be shown (For more information see Chapter 17 “Motifs and Features”.) If you want to assign a GenBank feature key, make a selection from the drop down menu called Feature Key. To give the feature a name, type your text into the Feature Name: box. You can use the default display style or you can assign a Feature Color and Feature Style, such as inverted case or underlined, from the dialog box. You can also use the Display: radio buttons to determine whether single stranded DNA is displayed or RNA, protein translation or the complement will be shown (For more information see Chapter 17 “Motifs and Features”.) Customizing your sequence view Formatting Ruler Formatting can be controlled with a ruler (shown in Figure 8-12) that lets you adjust several display parameters. Click the Ruler button in the Sequence Editor or contig Summary Window. Alternately you can go the View menu and choose Display Format Ruler. Figure 8-12 The formatting ruler Margins You can drag the margin triangles on this ruler to set the width of your sequence. Figure 8-13 shows margins that are limited to 42 bases per line. Figure 8-13 Sequence Editor with ruler and translations SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 58
The sequence margins you set with the formatting ruler are not the same as your absolute print margins, which allow room at the left to show the first base number of a line. To change the absolute limits, go to the File menu and choose Set Header & Footer… and enter new values into the Margin boxes or drag the triangular markers just under the Translation and Base Grouping icons, as shown in Figure 8-13 above. Translation On the left, just under the word “Residue” and above the ruler, is a set of three small icons that let you specify sequence representation: single-stranded, double-stranded, or single-stranded with a protein translation. If you select the third ‘translation’ icon, the numbered button at the right controls which frame or whether all three frames will be displayed. You can also use the translation commands in the Translation submenu of the View menu: Single Stranded, Double Stranded, Protein 1st Frame, Protein 2nd Frame, Protein 3rd Frame, or Protein All 3 Frames (see Figure 8-14). Figure 8-14 Translation icons on the Formatting ruler See Chapter 21, “Customizing Sequencher and User Preferences” for information on editing the genetic code or using one-letter abbreviations for amino acids. Base grouping To the right of the translation display icons are the icons that let you choose blocking, the number of bases to be displayed in a single group. The available settings are 3, 5, 10, 20 and Fill-to-margin. In Figure 8-14 above, the icon for a grouping of 10 is selected. Line spacing You can choose single, double or triple line spacing. The three small icons that let you control the line spacing are located to the right of the base grouping icons. Figure 8-14 above shows the icon for single spacing selected. Case and Font To the right of the line spacing icons is a pair of icons that let you choose upper or lower case for the display. In Figure 8-14 above, the icon for upper case is selected. To the right of the upper and lower case icons is a pull down menu, which lets you choose a font and size. Only fixed-width fonts are displayed, ensuring that the rows of bases will line up vertically. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 59
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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 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 70 and 71: Viewing summary information in the
Page 72 and 73: Figure 8-7 ORF selected by Next Met
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
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
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
Page 120 and 121: Structure of the Translated Varianc
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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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