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

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If you want to restrict the Comparison Range, click the Filter Translation by: radio button. Once you have clicked the Filter Translation by: radio button the Feature Key: drop down menu becomes active. You can now choose which Filter Key to use by making a selection from this menu. Once you have selected a Feature Key, you will see a list of features annotated with that key in the pane located below the Feature Key: drop down menu. You can select a single feature, a continuous range or a discontinuous range of features. You can also select all the features within this pane by clicking on the Select All button. Once you have made your selection click the OK button. The Translated Variance Table will be rebuilt automatically (see Figure 13-10). Figure 13-10 Translated Variance Table restricted by Translation Range The table header indicates how the Comparison Range was restricted. For some Feature Keys the actual feature is composed of several components joined together (see Figure 13-9). The Base Positions indicate the exact range of bases used for each component. Features which share the same Feature Key, such as CDS, and which are joined (the Feature has a Join qualifier) will appear in the Feature Listing as CDS [01], CDS [02]. The same Feature will appear in the Translation Range dialog window as a single item (see Figure 13-11). See Chapter 17 “Motifs and Features” and Appendix 28 “Feature Keys and Qualifiers” for more information. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 110
Figure 13-11 Feature key with more than one component If you prefer to have each component of a Joined Feature as a separate item you must give them different names. You can do this by editing the Feature using the Edit Features… command (see figure below). Figure 13-12 Appearance of features once they have been renamed You can also create your own joined features. Use the Edit Features… command to create a series of features which share the same name followed by a bracketed number, CDS [01], CDS [02] (see Figure 13-13). SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 111
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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
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
Page 106 and 107: Consensus to Forensic Standards In
Page 108 and 109: consensus is from a base with a low
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
Page 120 and 121: Structure of the Translated Varianc
Page 122 and 123: (see Figure 13-5). It is possible f
Page 124 and 125: Figure 13-7 Translated Variance Tab
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
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
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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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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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