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

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Figure 3-1 An empty Sequencher Project Window Until you create or import sequence fragments, the new project will remain empty. As you add sequences to your project and build contigs from them, the Project Window begins to look more like Figure 3-2. Figure 3-2 A new project All the sequences and contigs added to this particular sequencing project are displayed in this window. Note: If you have so many open windows on the screen that it’s difficult to find the Project Window, go to the Window menu and click on Project Window. This will bring the current project to the front. As you work, if you close an existing project and then want to start a new project, go to the File menu and choose New Project. Sequencher will open a new untitled project. Sequencher will remember the last projects you opened. You can see these as a list by going to the File menu and selecting the Open Recent command. Opening an existing project To open an existing project, go to the File menu and choose Open Project to select the project you want to work with. Click the Open button in the lower right area of the dialog box, or click the Return key. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 10
Working with items in the Project Window To work with items in the Project Window, first select the item(s) you need by clicking on them. Then choose the appropriate menu command. Icon types In the Project Window a sequence is represented by an autorad icon. However, there are other data types you may have in your project. To get familiar with some of the icons Sequencher uses for these data types, see Figure 3-3 Figure 3-3 Examples of Sequencher icons A sequence fragment A sequence fragment with edited comments A contig A refrigerator A Reference Sequence A sequence in the inverse-complement orientation Other information may be displayed in addition to the basic icon. For example, the downward-pointing arrow on a sequencing image icon shows that this sequence is stored in its original orientation (the sequence travels “down” the gel). The arrow points up when the data is inverse-complemented as shown in Figure 3-3. Project views View as Large Icons To display large icons in your Project Window, go to the View menu and then choose Project Icons As. Then select Large Icons from the submenu. The Project Window then displays the sequences and contigs as shown in Figure 3-4. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 11
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 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 74 and 75: 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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When you use a Name Delimiter, it w
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If the Expression is a delimiter bo
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Figure 10-6 The Project Window with
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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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