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

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Page Intentionally Left Blank SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 178
21. Customizing Sequencher and User Preferences In this chapter we discuss how to set your view preferences, such as colors, custom codes, features and motifs and the genetic codes you want to use. We also discuss how to set your user preferences such as confidence scores, labels and names, assembly parameters and how you want to display chromatograms. You will learn that all of these preferences can be saved as individual or group preferences. View Preferences Sequencher offers you a number of options for specifying how you want to view your data in the sequence and contig editors. These options can provide visual cues which help to differentiate your data. Ambiguous bases Sequencher can underline all ambiguous bases in the sequence or contig editors. Go to the View menu and choose Base Ambiguities As. Go to the submenu and choose Underlined to mark ambiguities or Not Highlighted for unmarked ambiguities. Edited Bases Sequencher can highlight bases that have been edited, which helps you audit the integrity of your data. Go to the View menu and choose Base Edits As. Select Not Highlighted for unmarked edits, Bold Magenta for colored edits and bOLD & cASE cHANGE for bold and a changed case. Display Color Bases Sequencher can display bases in color. To turn on this feature for either a sequence or contig editor display, choose Display Color Bases from the View menu. (For information on how to change the color assignments see the section “Ambiguity Codes” in this chapter.) SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 179
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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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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
Page 144 and 145: If you prefer to copy your Translat
Page 146 and 147: You can copy your Translated Varian
Page 148 and 149: Summary report display options Sequ
Page 150 and 151: Enabling the protein display To ena
Page 152 and 153: Page Intentionally Left Blank SEQUE
Page 154 and 155: Note: Remember that even if a seque
Page 156 and 157: If you select the Contig Chromatogr
Page 158 and 159: Select command Table 15-1 Summary o
Page 160 and 161: Note: The Extend Selection command
Page 162 and 163: Figure 16-2 Restriction map options
Page 164 and 165: example, if you were displaying onl
Page 166 and 167: Figure 16-8 Checkmarked enzyme list
Page 168 and 169: display this view by going to the V
Page 170 and 171: The default setting shows exact mat
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
Page 182 and 183: a dialog box (Figure 18-6). This le
Page 186 and 187: Figure 19-1 Export Options dialog b
Page 188 and 189: You should remember to provide a re
Page 190 and 191: Figure 19-3 Copy As Protein Transla
Page 192 and 193: [Project Name] and [User Name]. You
Page 196 and 197: Colors as Backgrounds Sometimes, di
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 204 and 205: Click the Use Blank Project radio b
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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