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

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Creating and editing features To create or edit features in a sequence, click on the sequence icon. Go to the Sequence menu and choose Edit Features… to display the Feature Editor (Figure 17-5). Figure 17-5 Feature Editor dialog box To create a new feature, click the Add button in the dialog box. From the Feature Key: menu choose Sequencher if you are creating personal annotations, or choose one of the GenBank keys. If you have chosen Sequencher as your Feature Key:, type a name in the Feature Name: field. Enter the starting and ending base numbers for the feature in the Feature Location boxes. The default strand is 5’-> 3’ but you can change this using the Complement check box. Use the Display Style pull down menu (Figure 17-6) to specify strand type, color, case and underlining. You may select one attribute from each of the four style categories. When you have finished entering or editing your features, click Done. If you have chosen a GenBank Feature Key:, Sequencher will insert a default name in the Feature Name: field using the Feature Key and Feature Qualifier. You may edit this if you wish. Enter the starting and ending base numbers for the feature in the Feature Location boxes. The default strand is 5’-> 3’ but you can change this using the radio button 3’ -> 5’. Use the Display Style pull down menu (Figure 17-6) to specify strand type, color, case and underlining. You may select one attribute from each of the four style categories. When you have finished entering or editing your features, click Done. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 156
Check the Display Feature in Editors checkbox and then go to the View menu and click on Display Features to have your feature appear in the sequence or contig editor and the associated overviews. When you set a feature to include Protein or DNA-RNA this will only be displayed in appropriate views. Figure 17-6 The display style menu Editing an existing feature To edit an existing feature, go to the Sequence menu and choose Edit Features… To display the Feature Editor, click on the name of the feature in the feature list. Use the Display Style pull down menu to specify new display attributes. You can also change the Feature Key:, edit the Feature Name: and the Feature Location:. For example, you could change a Sequencher annotation into a GenBank feature. If you want to remove a feature, select its name from the list and click on the Remove button. When you have finished entering or editing your features, click Done. The features will appear in the Sequence Editor if you have checked the Display Features in Editors checkbox and Display Features in the View menu. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 157
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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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Page 124 and 125: Figure 13-7 Translated Variance Tab
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Page 128 and 129: Figure 13-13 Creating a Joined feat
Page 130 and 131: In either case, the method you choo
Page 132 and 133: You can edit your data directly in
Page 134 and 135: Figure 13-17 The Translated Varianc
Page 136 and 137: Figure 13-19 Extract from Variance
Page 138 and 139: The Population Table lists the vari
Page 140 and 141: If you want to remove sample sequen
Page 142 and 143: 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
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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 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 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
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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 214 and 215: Figure 22-1 The Validate mtDNA Prof
Page 216 and 217: Figure 22-3 The Circular Genome Siz
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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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