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

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The Bases View ................................................................................................................. 86 Working in the Bases View ....................................................................................................................... 86 Viewing sequence names .......................................................................................................................... 88 Before you start to edit ...................................................................................................... 88 Setting the base numbering ....................................................................................................................... 88 Consensus calculation ............................................................................................................................... 88 Consensus Inclusively ............................................................................................................................... 89 Consensus By Plurality ............................................................................................................................. 89 Consensus to Forensic Standards .............................................................................................................. 90 Assigning a Reference Sequence .............................................................................................................. 90 12. EDITING CONTIGS .................................................................................... 91 Finding bases which need attention .................................................................................. 91 Viewing an individual sequence from the contig ...................................................................................... 91 Finding disagreeing ambiguities ............................................................................................................... 91 Finding Disagreeing Bases ........................................................................................................................ 92 Finding Low Confidence Bases ................................................................................................................ 92 Finding Edited Bases................................................................................................................................. 92 Performing edits ................................................................................................................ 92 The Edit Command ................................................................................................................................... 92 Editing modes............................................................................................................................................ 93 Viewing Base Edits ................................................................................................................................... 93 Collect Gaps .............................................................................................................................................. 93 Moving Bases and Gaps ............................................................................................................................ 94 Using ReAligner to clean up contigs ........................................................................................................ 94 Moving sequences ..................................................................................................................................... 95 Deleting bases ........................................................................................................................................... 95 Deleting bases from the 5’ or 3’ ends ........................................................................................................ 96 Inserting gaps or bases into a contig ......................................................................................................... 96 Making edits from the consensus line ....................................................................................................... 96 Split After Selection… .............................................................................................................................. 97 Auto Match................................................................................................................................................ 97 Create new sequence from a consensus .................................................................................................... 98 Removing sequences from a contig .......................................................................................................... 99 Dissolving a contig .................................................................................................................................... 99 13. THE VARIANCE TABLE .......................................................................... 101 The Variance Table Strategy ........................................................................................... 101 What is a Variance Table ......................................................................................................................... 101 The Variance Table and consensus sequences ......................................................................................... 101 The Translated Variance Table ................................................................................................................ 102 The Structure of the Variance Table ........................................................................................................ 102 Structure of the Translated Variance Table.............................................................................................. 104 Creating a Variance Table ............................................................................................... 105 Variance Table for sequences in the same contig .................................................................................... 105 The consensus Variance Table ................................................................................................................. 105 Translated Variance Table for sequences in the same contig .................................................................. 106 The Translated consensus Variance Table ............................................................................................... 107 ix
Setting the Variance Table Conditions ............................................................................ 108 Restricting the Comparison Range.......................................................................................................... 108 Restricting the Translation Range ........................................................................................................... 109 Setting the Variance Table Display Options ............................................................................................ 112 Setting the Consensus Calculation for a Variance Table ......................................................................... 113 Variance Table Options ........................................................................................................................... 114 Working with the Variance Table .....................................................................................114 Navigating a Variance Table.................................................................................................................... 114 Sorting the Variance Table ...................................................................................................................... 114 Removing columns from the Variance Table .......................................................................................... 115 Review Mode .......................................................................................................................................... 115 The Review Mode and Compare Consensus to Reference ..................................................................... 116 The Review Mode and the Translated Variance Table ............................................................................ 117 The Review Mode and Sister Tables ....................................................................................................... 118 Variance Table Reports ....................................................................................................119 Variance Table Report ............................................................................................................................. 119 Individual Variance Reports .................................................................................................................... 120 Variance Detail Report ............................................................................................................................ 121 Population Report.................................................................................................................................... 121 Working with Variance Table Reports ............................................................................ 122 Printing a Variance Table Report............................................................................................................. 122 Printing selected data from a Variance Table .......................................................................................... 123 Exporting a Variance Table Report ......................................................................................................... 125 Exporting selected sample sequences ..................................................................................................... 125 Exporting data for selected variants ........................................................................................................ 126 Translated Variance Table Report ................................................................................... 127 Translated Variance Table Report ........................................................................................................... 127 Working with a Translated Variance Table Report.......................................................... 127 Exporting a Translated Variance Table Report ........................................................................................ 127 Exporting selected sample sequences ..................................................................................................... 128 Exporting data for selected variants ........................................................................................................ 129 Removing data from a table before export .............................................................................................. 130 14. THE SUMMARY REPORT .......................................................................131 The Summary Report view ............................................................................................. 131 View by Summary ................................................................................................................................... 131 Summary report display options ..................................................................................... 132 Compare To Consensus or Reference Sequence ..................................................................................... 132 Icons ........................................................................................................................................................ 132 Bullets, Pluses and Dashes ...................................................................................................................... 133 Consensus Sequence ............................................................................................................................... 133 Fragment Sequences................................................................................................................................ 133 Matching Bases as Dashes ...................................................................................................................... 133 Protein translations and the Summary Report ................................................................ 133 Enabling the protein display.................................................................................................................... 134 x
Page 2 and 3: THIS IS AN AGREEMENT BETWEEN YOU, T
Page 4 and 5: © 1991 - 2007 Gene Codes Corporati
Page 6 and 7: Templates .........................
Page 8 and 9: Set Circular Genome Size ..........
Page 12 and 13: Protein translations for the Consen
Page 14 and 15: Setting header, footer and margin o
Page 16 and 17: Page Intentionally Left Blank xv
Page 18 and 19: We welcome your comments or support
Page 20 and 21: Navigating Sequencher Help The Sequ
Page 22 and 23: Contig menu The commands in the Con
Page 24 and 25: Page Intentionally Left Blank SEQUE
Page 26 and 27: Figure 3-1 An empty Sequencher Proj
Page 28 and 29: Figure 3-4 Project Window with Larg
Page 30 and 31: value in the Confidence pane of the
Page 32 and 33: Editing the information for a seque
Page 36 and 37: How to import using menu commands I
Page 38 and 39: Figure 4-2 Browse for Folder dialog
Page 40 and 41: Importing Confidence Scores Many ba
Page 42 and 43: If you have finished working with S
Page 44 and 45: Selecting sequences Selecting seque
Page 46 and 47: Renaming a sequence or contig Renam
Page 48 and 49: Closing the Project Window When you
Page 50 and 51: Performing a trim with default sett
Page 52 and 53: additional control within the Trim
Page 54 and 55: Figure 6-7 The polylinker window No
Page 56 and 57: 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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Page Intentionally Left Blank SEQUE
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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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Note: The Extend Selection command
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Figure 16-2 Restriction map options
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example, if you were displaying onl
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Figure 16-8 Checkmarked enzyme list
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display this view by going to the V
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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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