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

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Set Circular Genome Size ......................................................................................................................... 51 Splitting a sequence................................................................................................................................... 51 Duplicating a sequence ............................................................................................................................. 52 Reverse and Complement ......................................................................................................................... 52 About experimental data ................................................................................................... 52 Creating a baseline .................................................................................................................................... 52 Resetting a baseline ................................................................................................................................... 53 Viewing experimental data ........................................................................................................................ 53 Reverting to experimental data ................................................................................................................. 53 Viewing experimental data for Chromatograms ....................................................................................... 53 Viewing summary information in the Sequence Editor ............................................................................ 54 Selecting Bases ................................................................................................................. 55 Finding Ambiguous Bases......................................................................................................................... 55 Finding Open Reading Frames (ORF) ...................................................................................................... 55 Sequence features .............................................................................................................. 56 Looking at codon maps ............................................................................................................................. 56 Looking at Restriction Maps ..................................................................................................................... 56 Annotating Sequences ............................................................................................................................... 57 Customizing your sequence view ..................................................................................... 58 Formatting Ruler ....................................................................................................................................... 58 Margins ..................................................................................................................................................... 58 Translation ................................................................................................................................................. 59 Base grouping............................................................................................................................................ 59 Line spacing .............................................................................................................................................. 59 Case and Font ............................................................................................................................................ 59 Voice verification .............................................................................................................. 60 Selecting a voice file ................................................................................................................................. 60 Identifying a speaker ................................................................................................................................. 60 Audible keystrokes .................................................................................................................................... 60 Read sequence selection ............................................................................................................................ 60 9. SEQUENCE ASSEMBLY .............................................................................63 The Assembly Strategy ..................................................................................................... 63 Setting the Assembly Conditions ...................................................................................... 64 Setting assembly parameters ..................................................................................................................... 64 Assembly Algorithms ................................................................................................................................ 64 Assembling with Dirty Data...................................................................................................................... 65 Assembling with Clean Data ..................................................................................................................... 65 Assembling with Large Gap ...................................................................................................................... 66 Refining the Assembly conditions .................................................................................... 67 Minimum Match Percentage ..................................................................................................................... 67 Minimum Overlap ..................................................................................................................................... 67 Maximum Loop Out Size .......................................................................................................................... 67 Optimization of gap placement ................................................................................................................. 67 vii
Performing the assembly ................................................................................................... 68 Automatic assembly .................................................................................................................................. 68 Adding selected items to others – incremental building of contigs .......................................................... 68 Assemble to Reference .............................................................................................................................. 68 Interactive assembly .................................................................................................................................. 69 Performing an interactive assembly .......................................................................................................... 69 Changing parameters for an interactive assembly .................................................................................... 72 Mindlessly Join ......................................................................................................................................... 72 10. ASSEMBLE BY NAME ..............................................................................73 Setting the Assemble by Name Conditions ....................................................................... 74 Configuring Assembly Handles using a Single Delimiter......................................................................... 74 Configuring Assembly Handles using Advanced Expressions.................................................................. 75 What is a regular expression ................................................................................................................... 75 Setting your Assembly Handle Names ...................................................................................................... 76 Choosing a New Assembly Handle ........................................................................................................... 77 Enabling Assemble by Name .................................................................................................................... 77 Setting Assembly Parameters .................................................................................................................... 78 Performing an Assembly with Assemble by Name ........................................................... 78 11. THE CONTIG EDITOR ...............................................................................81 Contig editing.................................................................................................................... 81 Overview of the contig ...................................................................................................... 81 The contig overview window .................................................................................................................... 81 Selection marquee ..................................................................................................................................... 82 Checking coverage in the Overview ......................................................................................................... 82 Overview features ............................................................................................................. 83 Bases ......................................................................................................................................................... 83 Summary ................................................................................................................................................... 83 Sort ............................................................................................................................................................ 83 Overview options .............................................................................................................. 83 Scale Diagram To Window Size ................................................................................................................ 84 Diagram Key ............................................................................................................................................. 84 Labels Of Fragments ................................................................................................................................. 84 Names Of Fragments................................................................................................................................. 84 Names Of Fragments, At Left ................................................................................................................... 84 Positions Of Fragments ............................................................................................................................. 85 Start & Stop Codons.................................................................................................................................. 85 Base Numbers At Transitions .................................................................................................................... 86 Base Numbers At Every x Bases ............................................................................................................... 86 Condensed Base Numbers......................................................................................................................... 86 Getting more information ................................................................................................. 86 Find ........................................................................................................................................................... 86 Get Info ..................................................................................................................................................... 86 viii
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 10 and 11: The Bases View ....................
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 34 and 35: Page Intentionally Left Blank 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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Page Intentionally Left Blank SEQUE
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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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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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