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

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(see Figure 13-5). It is possible for a sequence to have partial coverage, a pink header and footer, but not have any pink X’s in the column. Note: When comparing multiple consensus sequences, the View menu’s Display Base Confidences option is not relevant, because confidence values exist only in fragments and not in consensus sequences. Figure 13-5 Compare Consensus to Reference Variance Table For more information about Assemble by Name and Reference Sequences, see Chapter 10 “Assemble by Name” and Chapter 7 “The Reference Sequence”. Translated Variance Table for sequences in the same contig When you are ready to begin creating your Translated 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 Translation To and either Consensus, Reference Sequence or Top Sequence from the submenu. The Translated Variance Table appears in a new window (see Figure 13-6). The Translated Variance Table header summarizes the table’s contents including a Description, the Base Positions and the Amino Acid Positions. If a sequence in the Table does not extend the full length of the Comparison Range, its column header will be shaded in pink. The pink X’s mark cells that are not covered by sequence data, indicating that the status of the base at that position is unknown. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 106
Figure 13-6 Translated Variance Table for sequences in the same contig The Translated consensus Variance Table Sequencher allows you to compare the translation of a consensus sequence to the translation of a Reference Sequence. Go to the Contig menu and click on Compare Translation to Reference. You can also use the Compare Translation to Reference command to compare the translations of consensus sequences from multiple contigs to the translation of their common Reference Sequence.. These contigs are formed when you use the Assemble By Name with a Reference Sequence command. For both of these operations, select one or more contigs in the Project Window that share a common Reference Sequence. Then, from the Contig menu, choose Compare Translation to Reference. The Translated consensus Variance Table appears in a new window (see Figure 13-7). SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 107
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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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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
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Page 114 and 115: First select the base or range of b
Page 118 and 119: The Translated Variance Table If yo
Page 120 and 121: Structure of the Translated Varianc
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
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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
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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 160 and 161: Note: The Extend Selection command
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Page 166 and 167: Figure 16-8 Checkmarked enzyme list
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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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