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

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Figure 19-3 Copy As Protein Translation options dialog box Alternatively, you can also go to the File menu. Click on the Export command and choose Selected Bases as Protein… from the submenu. You will be presented with a window similar to that above (see Figure 19-3). You will then be prompted with a Save As: window. Export Overviews If you are looking at the schematic view of a contig, you can generate a text version map of the fragments, as shown in Figure 19-4, for viewing in other programs or word processors. There are two ways to do this. 1. Go to the File menu and choose Export, then Overview as Text from the submenu. Sequencher will treat the map as any other exported file. 2. Alternatively, you can copy the overview as a picture and paste it into other programs. Select the overview window by clicking on it, then go to the Edit window and choose Copy As and Picture from the submenu. Note: When viewing the output, you must specify a fixed-width font to preserve the scale of the arrows in relation to each other and the fragment names. Figure 19-4 ASCII map of sequence Exporting contig summaries When you are displaying the Summary view of a contig (see “Summary Report View” in Chapter 12, “Editing Contigs”), you can export the contents of the report to a text file. Go to the File menu and choose Export then the Summary… submenu. This is particularly useful if you wish to add annotations to a report of your assembly in standard page format. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 174
20. Output In this chapter we discuss printing options. We will explain how to set up pages, copy pictures, print and use different report formats. Copy picture Sequencher can copy the images from many of its windows, including text windows, to a picture on the clipboard. Select the window you want copied, go to the Edit menu and choose Copy As then click on Picture. Print setup Before printing, go to the File menu and choose Print Setup… to change the options that are specific to your printer. Some options that may be available on your printer include portrait or landscape printing (vertical or horizontal orientation), paper size, reduction, enlargement, or special handling for color printing. (See Chapter 21, “Customizing Sequencher and User Preferences” for more information.) Print Trace in One Page This command appears within the File menu and allows you to print an individual trace so that the entire sequence fits on one page. Printing in detail Most windows that contain data can be printed. To print, select a window by bringing it to the front. Then go to the File menu and choose Print and enter your print specifications. Setting header, footer and margin options Specify header, footer and margins for any printout by going to the File menu and choosing Set Header & Footer…. You enter the text of the header and footer and a code style for elements into a dialog box (Figure 20-1) that Sequencher will automatically increase incrementally. The code elements are [Date], [Time], [Page], [Total Pages], SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 175
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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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additional control within the Trim
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Figure 6-7 The polylinker window No
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Setting Vector Trimming Criteria Se
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Basic Reference Sequence properties
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When the To Reference by Name comma
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A locked editor is read-only. You c
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If your sequence was called “MyPU
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Viewing summary information in the
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Figure 8-7 ORF selected by Next Met
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If you want to assign a personal an
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Voice verification Sequencher provi
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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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Page 160 and 161: Note: The Extend Selection command
Page 162 and 163: Figure 16-2 Restriction map options
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Page 166 and 167: Figure 16-8 Checkmarked enzyme list
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Page 172 and 173: Creating and editing features To cr
Page 174 and 175: Quick feature creation To create a
Page 178 and 179: Figure 18-1 A dimmed icon Finding t
Page 180 and 181: Note: If you pause between characte
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Page 186 and 187: Figure 19-1 Export Options dialog b
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Page 198 and 199: Choosing a genetic code You will fi
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Page 202 and 203: Label & Name The Label & Name prefe
Page 204 and 205: Click the Use Blank Project radio b
Page 206 and 207: Use the Columns For Multiple Traces
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Page 210 and 211: Variance Table The Variance Table p
Page 214 and 215: Figure 22-1 The Validate mtDNA Prof
Page 216 and 217: Figure 22-3 The Circular Genome Siz
Page 220 and 221: Menu/Window Command Windows Select
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Page 226 and 227: Code Base(s) Meaning 5 A or Another
Page 228 and 229: Feature Display Color Style Second
Page 232 and 233: eferences numbers, sequences, or us
Page 234 and 235: Qualifier type Description Citation
Page 236 and 237: Feature Key Default Feature Qualifi
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Name CursorProject Window Dialog bo
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