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

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Contig menu The commands in the Contig menu facilitate most of your work in contig editing. You can set assembly parameters and consensus mode, assemble, dissolve and rename your contigs, reposition sequences, remove selected sequences and Fill Coverage Gaps with the Reference Sequence or Trim to Reference Sequence. Sequence menu The commands in the Sequence menu facilitate most of your work in sequence editing. You can set up data entry preferences such as trimming poor quality data or vector contamination, edit features, create and rename sequences, set up a Reference Sequence, set up base numbering and Revert To Experimental Data. View menu The commands in the View menu let you control how data is displayed as you work on it. You can add extra information to the display, specify the format and marking of the data and organize project files from the View menu. Some of the functions in the View menu have options, which you can change by going to User Preferences (see Chapter 21 “Customizing Sequencher and User Preferences”, for more information). Window menu The commands in the Window menu offer access to different kinds of user help, to reference information on various aspects of your data, to different windows you have opened and to User Preferences. Help menu The command in this menu offers access to user help. Context Sensitive menus and buttons Sequencher has a number of menus and buttons that may change depending on the context. Some items will become enabled. The labels of other items will change. This feature is designed so that Sequencher can offer you extensive options within the same easy-to-use interface. Contextual menus Most windows in Sequencher offer contextual menus. You can invoke these by clicking within the window you are reading while holding down the right hand mouse button. If you select one or more items and then click the right hand mouse button, you will see other menus. Note: If you have a mouse with only one button, you may be able to mimic the effect of a right hand button with the use of a modifier key. SEQUENCHER 4.8 User Manual for Macintosh © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 6
Keyboard shortcuts Sequencher has a number of keyboard shortcuts for major menu items and other important features and allows you to define some of your own. See Appendix 23 “Keyboard Shortcuts” for a complete listing. See Chapter 21 on “Customizing Sequencher and User Preferences” for more information about how to define your keyboard shortcuts. SEQUENCHER 4.8 User Manual for Macintosh © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 7
Page 2 and 3: THIS IS AN AGREEMENT BETWEEN YOU, T
Page 4 and 5: © 1991 - 2007 Gene Codes Corporati
Page 6 and 7: Templates .........................
Page 8 and 9: Set Circular Genome Size ..........
Page 10 and 11: The Bases View ....................
Page 12 and 13: Protein translations for the Consen
Page 14 and 15: 21. CUSTOMIZING SEQUENCHER AND USER
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Page 18 and 19: We welcome your comments or support
Page 20 and 21: Navigating Sequencher Help The Sequ
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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: If you are working with ABI sequenc
Page 32 and 33: Figure 3-10 The Get Info window If
Page 36 and 37: How to import using menu commands I
Page 38 and 39: Sequencher tells you how many files
Page 40 and 41: Double-clicking a project icon When
Page 42 and 43: Closing a project If you have finis
Page 44 and 45: Selecting sequences Selecting seque
Page 46 and 47: Renaming a sequence or contig Renam
Page 48 and 49: the close box. In either case, Sequ
Page 50 and 51: will be a checkbox at an end if it
Page 52 and 53: Figure 6-4 Bases view in Ends 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: Name button will only be displayed
Page 66 and 67: Basic sequence editing The Sequence
Page 68 and 69: Duplicating a sequence You can dupl
Page 70 and 71: Figure 8-5 Sequence information win
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Figure 8-8 Sequence Editor with cod
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If you want to assign a personal an
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Voice verification Sequencher provi
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Page Intentionally Left Blank SEQUE
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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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However, a Name Delimiter can also
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Figure 10-3 Advanced Expression for
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Once you have clicked on the AbN bu
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it is in the reverse orientation. T
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turn this option off, you make the
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You can use the Any Ambiguous Base
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Label Name Function I Ambiguities D
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• If there are two or more disagr
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consensus is from a base with a low
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move the gaps to the 5’ end, sele
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You can also perform the deletion b
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match a high quality segment of seq
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. Page Intentionally Left Blank SEQ
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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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translations. Alternately, you can
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Note: Remember that even if a seque
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clicking any of the buttons to hide
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Table 15-1 Summary of Select comman
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When you are looking at a chromatog
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A dialog box (Figure 16-2) lets you
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Getting more information about an e
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You can now enter information in th
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The default setting shows exact mat
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Features What is a feature A featur
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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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Set the margins by typing appropria
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Colors as Backgrounds Sometimes, di
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Choosing a genetic code You will fi
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Layout. Select the submenu option c
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Figure 21-6 Confidence Ranges: sett
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Figure 21-9 Sound preference settin
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Figure 21-11 Chromatogram preferenc
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Figure 21-14 Contig preference sett
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Figure 21-16 Format ruler preferenc
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Figure 21-19 File import preference
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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 Mac Select Ne
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Menu/Window Command Mac 2 cutters C
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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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For a more detailed discussion of t
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Table 27-2 Feature Qualifiers Quali
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Feature Key Default Feature Qualifi
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Name CursorProject Window Dialog bo
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