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

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Summary report display options Sequencher has a default format for the summary report but you can change it to display different types of information. Click the Options button or go to the View menu and choose View Options… The Summary Options are divided into those that affect the sequence fragments and those that affect the display of protein translations. You can change the consensus calculation while in this view. Any change you make will be reflected immediately in the report. Sequencher displays the window shown in Figure 14-1. Figure 14-1 Summary report options Compare To Consensus or Reference Sequence If you have a Reference Sequence in your contig you can choose whether to display a Summary Report compared to the consensus sequence or to the assembled Reference Sequence. The default setting is Compare To: Consensus but you can change this by clicking on the Reference radio button. Some of the Display options are context sensitive and will change to reflect your choice. The Reference radio button will be grayed out when the selected contig does not contain a Reference Sequence. Icons If you check the box for the Icons display, you will see the sequence fragment icons positioned to the left of the fragment name. Unchecking this option will hide the icons. Note: When you have a Reference Sequence in your contig its icon is distinguished by the addition of an “R”. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 132
Bullets, Pluses and Dashes Clicking the Bullets, Pluses boxes highlights disagreements and ambiguities in a line below the consensus. If you also click on & Dashes you are marking positions where the bases in individual fragments match so that the disagreements are more visible. Note: You can display Bullets, Pluses without the & Dashes but you cannot display & Dashes without the Bullets, Pluses. However, see Matching Bases As Dashes below. Consensus Sequence You can choose to hide the consensus sequence by clicking on the Consensus Sequence box. Figure 14-2 shows a summary line without the consensus line but with Bullets, Pluses and & Dashes all checked. Figure 14-2 Summary report with no consensus line, with bullets, pluses and dashes Fragment Sequences You can choose to hide the fragment sequence by clicking on the Fragment Sequences box. This gives you a very compressed report that can be useful when viewing protein translations. Figure 14-2 above shows a summary line without the consensus line, but with Bullets, Pluses and & Dashes all checked. Matching Bases as Dashes Matching Bases As Dashes is a very powerful option when you are interested in any kind of mutation detection. When you check this option all the bases that match each other are converted to dashes. If you have selected Display Color Bases the dashes will be marked in the color of the original base call. If you also go to the View menu and chose Colors as Background, each dash will appear embedded in a small color block. Bases that disagree are displayed as characters and as such stand out in stark relief. With this option, you can easily see mutation hot spots or clusters and potential SNPs. Protein translations and the Summary Report Sequencher can show protein translations for individual fragments and mark matching amino acids with dashes. This helps you see whether a particular discrepancy in an alignment has functional implications or whether it may simply be a silent mutation. If you combine options, you can turn off the DNA display altogether and just focus on your translations. Alternately, you can use a mixture of options to tailor the report to your specific needs. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 133
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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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Page 98 and 99: it is in the reverse orientation. T
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 116 and 117: Page Intentionally Left Blank SEQUE
Page 118 and 119: The Translated Variance Table If yo
Page 120 and 121: Structure of the Translated Varianc
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Page 124 and 125: Figure 13-7 Translated Variance Tab
Page 126 and 127: If you want to restrict the Compari
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 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
Page 178 and 179: Figure 18-1 A dimmed icon Finding t
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Page 186 and 187: Figure 19-1 Export Options dialog b
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Page 190 and 191: Figure 19-3 Copy As Protein Transla
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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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