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

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Click the Use Blank Project radio button if you want your New Project to be blank. Click the Use Project Template radio button if you want the project settings to be controlled by a template. Specify the template you want by clicking on a name in the drop down menu. Templates are stored in a folder on your system. If you click the Open Templates Folder button Sequencher will open a window displaying the templates. You can store up to 1,000 templates on your system. (For more information about templates, see Chapter 3, “The Project Window.”) Figure 21-10 New Project User Preferences Display Chromatogram Chromatogram preferences control the display of chromatograms. You can specify the Height Of Chromatograms by clicking one of the buttons from Tiny to Tall. If you use a black and white monitor, click the Pattern button for Lane Identification By;. You can set lanes to be identified by color or pattern by selecting the appropriate radio button. When viewing multiple sequences, you will notice that a reversed and complemented sequence displays the lane colors according to the original data. Click the Colors Match Current Bases checkbox to display all current base calls in the same color. Click the Hide Original Base Calls checkbox if you do not want them to appear in your chromatogram windows. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 188
Figure 21-11 Chromatogram preference settings If you click the Print Scale Factor checkbox and you used the slider shown at the left in Figure 21-12, the scale factor will appear on any printout of that chromatogram. If you click the Rev & Comp Displayed as Lower Case checkbox, the original base calls for a reversed and complemented sequence are shown in lower case (as opposed to backwards) as the second of two lines of bases above the traces (as in Figure 21-12). Figure 21-12 Reversed and complemented sequence Under Width Peak to Peak, you can stretch your traces horizontally by selecting the Wide button. Contig Chromatogram The Contig Chromatogram preferences control the display of chromatograms of sequences from a contig. When you have aligned several sequences from a contig and displayed the chromatograms, several traces appear in a single window, one above the other across the width of the window. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 189
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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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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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Page 154 and 155: Note: Remember that even if a seque
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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
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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 190 and 191: Figure 19-3 Copy As Protein Transla
Page 192 and 193: [Project Name] and [User Name]. You
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Page 198 and 199: Choosing a genetic code You will fi
Page 200 and 201: time you select the Review button f
Page 202 and 203: Label & Name The Label & Name prefe
Page 206 and 207: Use the Columns For Multiple Traces
Page 208 and 209: If you are making changes to the wa
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
Page 222 and 223: You may require a more complex deli
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
Page 240 and 241: Name CursorProject Window Dialog bo
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