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

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Renaming a sequence or contig Renaming using the mouse To rename a sequence fragment or contig with the mouse, click twice on the name of the item. This selects the icon and puts a text box around the name. Just type in the new name and when you are done, click elsewhere in the Project Window. If you only want to change part of the name, drag the cursor over what you want to replace and then type the replacement text in the highlighted area. You can also use the Copy and Paste functions to rename sequences. Renaming using the menu If you wish to rename a sequence you can go to the Sequence menu and choose the Rename Sequence… command. To rename a contig, go to the Contig menu and click on the Rename Contig… command. Sequencher displays a dialog box (Figure 5-2) with a field for you to enter the new name. Click the OK button when you have finished. Figure 5-2 Renaming a sequence Labeling items in the Project Window You can organize items visually in the Project Window by applying Labels to the icons. Before using Labels for the first time, you should customize the list of labels under the General section of User Preferences. You will see a list of Label & Name options. You can also select from the default labels available under the Edit menu and Label submenu. (See Chapter 21 “Customizing Sequencher and User Preferences” for more information.) When viewing your project as a list, you will see the name of the label in the list. Labeling your icons allows you to sort or find your information easily. For instance, you might define red labels as cDNA data and blue labels as genomic data. Clicking on the label heading in the Project Window will sort your project items by label (see Figure 5-3). You can also find sequences bearing a particular label by going to the Select menu and choosing the All Items That command with the Have Labels Containing… suboption. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 30
Figure 5-3 Viewing labels as a list Saving your work Saving your Project To save a project go to the File menu and choose Save Project, which saves all your changes to the current project file. When you use the Save Project command for a new project, Sequencher will prompt you to name your project with the Save As dialog. Enter a name for the new project in the File name: field then click Save. Auto-Save If you are working on complex projects you may find it helpful to have Sequencher automatically save your work at pre-set time intervals. You will need to enable the Auto- Save user preference from User Preferences… in the Window menu. (See the Chapter 21 “Customizing Sequencher and User Preferences” for more details.) Saving a duplicate of a current project If you wish to create a second copy of a current project you can use the Save Project As… command to create the new copy of your project with a different name. When you save the new project, a new project icon appears on your disk. Reverting to the saved version of the project. If you are working in a project and want to cancel all the changes you have made since you last saved it, go to the File menu and choose Revert To Saved Project… Sequencher displays a dialog box that tells you when your project was last saved. If you click the Yes, Revert to Saved Version button you will lose the most recent changes. Click on the Cancel button to cancel the command. Note: Remember, if you click the Yes, Revert to Saved Version button you cannot undo this action. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 31
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: Setting header, footer and margin o
Page 16 and 17: Page Intentionally Left Blank xv
Page 18 and 19: 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
Page 24 and 25: Page Intentionally Left Blank SEQUE
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 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 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 Intentionally Left Blank SEQUE
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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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Consensus to Forensic Standards In
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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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Figure 12-4 Fill Void dialog box De
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First select the base or range of b
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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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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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