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

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Structure of the Translated Variance Table The structure of the Translated Variance Table follows the format of the Variance Table but its display consists of an amino acid and its codon in each cell (see Figure 13-3). When you see a cell in the table with an amino acid and its codon written in black typeface, this indicates a difference between your exemplar and your sample. You may also see some cells in the table where the amino acid and codon are displayed in light gray. Amino acids in these cells match the exemplar but use either an identical or synonymous codon. The numbers which appear in the first column of the Translated Variance Table refer to the position of the first base of the codon (in the upper location) and the position of the amino acid (in the lower one). Figure 13-3 The Translated Variance Table Note: When Sequencher encounters a gap, it skips to the next available base to include it as a component of the codon. If an N is in the first or second position of the codon, Sequencher displays a question mark () instead of an amino acid. If the N is in the third position of the codon, a residue may be displayed. This will depend on the genetic code redundancy. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 104
Creating a Variance Table Variance Table for sequences in the same contig When you are ready to begin creating your Variance Table, either select individual sequences from within a contig, or go to the Project Window and select a contig by clicking on its icon. This will select all of the contig’s sequences. Then go to the Sequence Menu and choose Compare Bases To and either Consensus, Reference Sequence or Top Sequence from the submenu. The Variance Table appears in a new window (Figure 13-4). Figure 13-4 Variance Table Created with Compare Bases To Reference Sequence The consensus Variance Table When you want to compare a consensus sequence to a Reference Sequence you use the Contig menu’s Compare Consensus to Reference command. You can also use the Compare Consensus to Reference command to compare the consensus sequences from multiple contigs that share the same Reference Sequence. These contigs are the result of using the Assemble By Name command with a Reference Sequence. For each of these operations, go the Project Window and select one or more contigs that share a common Reference Sequence. Then, from the Contig menu, choose the Compare Consensus to Reference command. The Variance Table appears in a new window (see Figure 13-5). Each cell in the resulting Variance Table will display a consensus base when that base differs from the Reference Sequence. Pink shading in the header and footer cells of the Variance Table highlight contigs where the consensus sequence does not cover the span of the Reference Sequence. The pink X’s mark specific cells where coverage is missing SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 105
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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
Page 70 and 71: Viewing summary information in the
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Page 74 and 75: If you want to assign a personal an
Page 76 and 77: Voice verification Sequencher provi
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Page 80 and 81: Chapter 9 “Sequence Assembly” f
Page 82 and 83: Figure 9-2 The Clean Data algorithm
Page 84 and 85: Performing the assembly Automatic a
Page 86 and 87: Figure 9-5 Interactive assembly sho
Page 88 and 89: The new contig will appear in the P
Page 90 and 91: When you use a Name Delimiter, it w
Page 92 and 93: If the Expression is a delimiter bo
Page 94 and 95: Figure 10-6 The Project Window with
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Page 100 and 101: Figure 11-2 Contig overview Fifure
Page 102 and 103: Base Numbers At Transitions Clickin
Page 104 and 105: Label Name Function E F G H Sequenc
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Page 110 and 111: move the gaps to the 5’ end, sele
Page 112 and 113: Figure 12-4 Fill Void dialog box De
Page 114 and 115: First select the base or range of b
Page 118 and 119: The Translated Variance Table If yo
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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
Page 150 and 151: Enabling the protein display To ena
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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The default setting shows exact mat
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Creating and editing features To cr
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Quick feature creation To create a
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Figure 18-1 A dimmed icon Finding t
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Note: If you pause between characte
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a dialog box (Figure 18-6). This le
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Figure 19-1 Export Options dialog b
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You should remember to provide a re
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Figure 19-3 Copy As Protein Transla
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[Project Name] and [User Name]. You
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Colors as Backgrounds Sometimes, di
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Choosing a genetic code You will fi
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time you select the Review button f
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Label & Name The Label & Name prefe
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Click the Use Blank Project radio b
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Use the Columns For Multiple Traces
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If you are making changes to the wa
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Variance Table The Variance Table p
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Figure 22-1 The Validate mtDNA Prof
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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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