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

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display this view by going to the View menu, selecting Bases, Map, Overview... and then choosing Restriction Map from the submenu. If you click between two cut sites, Sequencher highlights the resulting restriction fragment. Hold down the Shift key and click in the rectangle between other cut sites. Your selection is extended from the original site you selected. When you return to the Bases view you will see that the sequence representing the chosen region has been highlighted also. (See Figure 16-9.). Figure 16-9 Fragment selected in map view and its equivalent bases highlighted Copying the map After you have made a selection in the restriction map, as in Figure 16-9 above, you can copy the bases between the two cut sites by going to the Edit menu and choosing Copy Selection. You can also copy the entire diagram for use in an illustration program by going to the Edit menu and choosing Copy As and Picture from the submenu. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 152
17. Motifs and Features In this chapter we describe Sequencher’s ability to locate and highlight subsequences that you specify as motifs. You will learn how to create, edit and display features and list a sequence’s features. Motifs Sequencher lets you define up to 12 patterns of 50 or fewer bases as motifs. Entering motifs You define new motifs by going to the Window menu and clicking on the Motif Definitions… command. Figure 17-1 Motif entry window SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 153
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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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Page 118 and 119: The Translated Variance Table If yo
Page 120 and 121: Structure of the Translated Varianc
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Page 124 and 125: Figure 13-7 Translated Variance Tab
Page 126 and 127: If you want to restrict the Compari
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
Page 150 and 151: Enabling the protein display To ena
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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
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Page 166 and 167: Figure 16-8 Checkmarked enzyme list
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
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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
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Menu/Window Command Windows Select
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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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