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

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If you are making changes to the way Feature Keys are currently displayed you can click on the Update Project… button to update your project. You can decide whether to apply the current styles, name or both to All features in your project. If you do not want to do so, just limit your choices to Selected features in your project by clicking the appropriate button. When you are finished, click on the Done button to return to User Preferences. Use one or more of the three Display Feature Numbering For check boxes to indicate which of the second-line features Complement Bases, RNA Bases, or Amino Acids should have its own numbering. Use the Motif Default Style pull down menu to set color, case and underlining style for new motifs. You can see a preview of the motif style in a box on the right hand side of the Motif Default Style preference pane. Figure 21-15 Features and motif preference settings Format Ruler The Format Ruler preferences controls the display defaults for any view which has a format ruler. These are just defaults; you can change these settings later from within a specific editor. When you click an icon in the sets of icons above the ruler, your selection is explained and confirmed in the panel below the ruler (Figure 21-16). For example, use the Preferred Bases per Line counter to increase or decrease the preferred number of bases in each line. Note that if you request a line length that will not fit on the printed page, Sequencher uses the maximum line length that will fit. If you want the margin to be automatically adjusted when you increase the size of a window, check the Auto-Adjust Margin if Window is Resized checkbox. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 192
Figure 21-16 Format ruler preference settings Start-Stop The Start-Stop preferences control the locating of open reading frames from an editor. Use the buttons grouped under On Codon Maps Highlight to indicate whether you want None, which gives you the plain map of start and stop codons. Use Any Start to Stop >= or Any Unstopped Run >= to give you a shaded box showing open frames of a length you specify. Figure 21-17 shows selections in the Start-Stop preference pane that will make Sequencher highlight ORFs beginning with a MET and longer than 60 bases. Figure 21-17 Start-stop codon preference settings Under Select Next MET To Stop, you can define the minimum length of ORF selections in a Sequence Editor. If you specify a minimum length here, for example 30 bases, the Next MET To Stop command under the Select menu in the Sequence Editor will change to read Next MET To Stop (>30b). SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 192
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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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Note: Remember that even if a seque
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If you select the Contig Chromatogr
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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 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
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Page 190 and 191: Figure 19-3 Copy As Protein Transla
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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
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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
Page 240 and 241: Name CursorProject Window Dialog bo
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