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

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a dialog box (Figure 18-6). This lets you select items in the Project Window where the search string is based on only part of the complete name. Figure 18-6 Contain Items With Names Containing… dialog box Have Chromatograms If you want to find out which fragments have a chromatogram or which contigs contain fragments with chromatograms, go to the Select menu and choose All Items That and then Have Chromatograms. Have Comments Containing… If you want to select all the sequences in the Project Window whose comments contain a specific text string, go to the Select menu and choose All Items That and then Have Comments Containing… to display a dialog box (Figure 18-7). Figure 18-7 Have Comments Containing… dialog box Have Labels Containing… If you want to select all the sequences in the Project Window whose label contains a specific text string, go to the Select menu and choose All Items That and then Have Labels Containing… to display a dialog box (Figure 18-8). Figure 18-8 Have Labels Containing… dialog box SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 166
Have Names Containing… If you want to select all the sequences in the Project Window whose names contain a specific text string, go to the Select menu and choose All Items That and then Have Names Containing… to display a dialog box (Figure 18-9). Figure 18-9 Have Names Containing…dialog box Were Edited On Or Since… If you want to select all the sequences and contigs in the Project Window that were edited on a specified day, go to the Select menu and choose All Items That and then Were Edited On Or Since… to display a dialog box. You can use the drop down menu to specify a preset day such as today, yesterday, 1 week ago or even 2 months ago. You can also type a date in the Find What: box. Note: You can also include items edited on all the days since a specific date by checking the And All Days Since box. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 167
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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
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 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 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
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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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