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

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Variance Table The Variance Table preferences control how ambiguous matches and large gaps will be treated. If you wish to include ambiguous matches in your table, click the Include Ambiguous Matches checkbox. If you wish to exclude large gaps from your table, click the Exclude Large Gaps checkbox. When you generate a Variance Table you would expect to have blank cells where the base at that position matches the exemplar. If you would like to see all bases across the comparison range whether they match or are different to the exemplar then click the Populate All Cells checkbox (see Figure 21-18). Figure 21-18 Variance Table preference settings Input/Output File Import File Import preferences control how Sequencher applies the automatic trim function to imported files. Use the checkboxes grouped under Add Imported Sequences To Trim Window to specify which sequences Sequencher should examine for poor quality ends and then trim. You can also specify how you want to resolve conflicts between the names of imported files and names stored with particular sequences. If you click the Prefer File Names To Data Names checkbox, Sequencher uses the file name. Clicking the Review Trim Parameters button displays the Ends Trimming dialog box, in which you can set trim criteria. (See Chapter 6, “Preparing your Data for Assembly,” for details.) SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 194
Figure 21-19 File import preference settings Report The Report preferences command controls the default page setup for report printouts. Use the fields in the Page Margins box to set the margins and gutter. Click Page Setup to open the printer page setup dialog box. The page setup settings will apply to all windows you open thereafter. Figure 21-20 Report margin preference settings You can specify headers and footers on reports generated from any window in which you are working. Any text you type into the field above the page layout will appear in the header and text you type in the field below the layout will appear in the footer. For variable elements (date, time, page and total number of pages), enclose the word— typed with an initial capital—in square brackets, as shown in Figure 21-20 above. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 195
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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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Select command Table 15-1 Summary o
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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 172 and 173: Creating and editing features To cr
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 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
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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