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

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Templates .......................................................................................................................... 17 Save Project As Template .......................................................................................................................... 17 New Project From Template ..................................................................................................................... 17 Import from Template ............................................................................................................................... 17 4. IMPORTING DATA ....................................................................................... 19 Quick and easy importing of data ..................................................................................... 19 Dragging and dropping files ...................................................................................................................... 19 Copy and paste .......................................................................................................................................... 19 How to import using menu commands ............................................................................. 20 Importing sequences.................................................................................................................................. 20 Importing GenBank features ..................................................................................................................... 20 Importing lists of sequences ...................................................................................................................... 20 Folder of sequences ................................................................................................................................... 21 Projects in specific formats ....................................................................................................................... 22 Sequencher projects .................................................................................................................................. 22 Files from VecBase ................................................................................................................................... 23 Creating a new sequence ........................................................................................................................... 23 Double-clicking a project icon .................................................................................................................. 24 Importing Confidence Scores .................................................................................................................... 24 Importing PHRED called data .................................................................................................................. 24 Importing PHRAP Files ............................................................................................................................ 24 Removing sequences and contigs from a project ...................................................................................... 25 Closing an editor window ......................................................................................................................... 25 Closing a project ....................................................................................................................................... 26 5. ORGANIZING PROJECT VIEWS ................................................................ 27 Working with icons and lists ............................................................................................. 27 Changing between project views .............................................................................................................. 27 Collecting sequences in refrigerators ........................................................................................................ 27 Selecting sequences .......................................................................................................... 28 Selecting sequences and contigs ............................................................................................................... 28 Selecting with the mouse .......................................................................................................................... 28 Selecting by typing .................................................................................................................................... 28 Selecting multiple items with a marquee .................................................................................................. 28 Selecting using menu commands ...................................................................................... 29 Selecting all icons ..................................................................................................................................... 29 Selecting all items containing sequence .................................................................................................... 29 Finding assembled sequences ................................................................................................................... 29 Renaming a sequence or contig ........................................................................................ 30 Renaming using the mouse ....................................................................................................................... 30 Renaming using the menu ......................................................................................................................... 30 Labeling items in the Project Window ...................................................................................................... 30 Saving your work .............................................................................................................. 31 Saving your Project ................................................................................................................................... 31 Auto-Save .................................................................................................................................................. 31 v
Saving a duplicate of a current project ...................................................................................................... 31 Reverting to the saved version of the project. ........................................................................................... 31 Closing the Project Window...................................................................................................................... 31 Exporting data ........................................................................................................................................... 32 Exiting the program................................................................................................................................... 32 6. PREPARING YOUR DATA FOR ASSEMBLY .............................................. 33 Removing undesirable data ............................................................................................... 33 Trimming poor quality data .............................................................................................. 33 Selecting and trimming fragment data ...................................................................................................... 33 Performing a trim with default settings ..................................................................................................... 34 Automatically selecting sequences for ends trimming .............................................................................. 34 How to set the Ends Trimming criteria ..................................................................................................... 34 Using Confidence to Trim Ends ................................................................................................................ 35 Reviewing the Trim ................................................................................................................................... 35 Sorting items ............................................................................................................................................. 36 Executing the trim ..................................................................................................................................... 36 Trimming vector contamination ........................................................................................ 37 Selecting sequences for Vector Trimming ................................................................................................. 37 Specifying a vector using VecBase ........................................................................................................... 37 Specifying the insertion site manually ...................................................................................................... 39 Saving and loading vector sites ................................................................................................................. 39 Setting Vector Trimming Criteria .............................................................................................................. 40 How Sequencher screens sequences ......................................................................................................... 41 Executing the trim command .................................................................................................................... 41 7. THE REFERENCE SEQUENCE .................................................................. 43 What is a Reference Sequence? ........................................................................................ 43 Why use a Reference Sequence? ............................................................................................................... 43 Reference Sequence properties ......................................................................................... 43 Basic Reference Sequence properties ....................................................................................................... 44 Working with a Reference Sequence ................................................................................ 45 How to mark a sequence as a Reference ................................................................................................... 45 Assemble to Reference .............................................................................................................................. 45 To Reference by Name .............................................................................................................................. 45 Trim to Reference ...................................................................................................................................... 46 Contig Editing with a Reference Sequence ............................................................................................... 46 Fill Coverage Gaps with Reference .......................................................................................................... 47 Reference Sequence Translation ............................................................................................................... 47 8. THE SEQUENCE EDITOR ........................................................................... 49 Opening an existing sequence for editing ................................................................................................. 49 Locked Editors .......................................................................................................................................... 49 Basic sequence editing .............................................................................................................................. 50 Setting the base numbering ....................................................................................................................... 50 vi
Page 2 and 3: THIS IS AN AGREEMENT BETWEEN YOU, T
Page 4 and 5: © 1991 - 2007 Gene Codes Corporati
Page 8 and 9: Set Circular Genome Size ..........
Page 10 and 11: The Bases View ....................
Page 12 and 13: Protein translations for the Consen
Page 14 and 15: 21. CUSTOMIZING SEQUENCHER AND USER
Page 16 and 17: Page Intentionally Left Blank
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: If you are working with ABI sequenc
Page 32 and 33: Figure 3-10 The Get Info window If
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Page 36 and 37: How to import using menu commands I
Page 38 and 39: Sequencher tells you how many files
Page 40 and 41: Double-clicking a project icon When
Page 42 and 43: Closing a project If you have finis
Page 44 and 45: Selecting sequences Selecting seque
Page 46 and 47: Renaming a sequence or contig Renam
Page 48 and 49: the close box. In either case, Sequ
Page 50 and 51: will be a checkbox at an end if it
Page 52 and 53: Figure 6-4 Bases view in Ends Trim
Page 54 and 55: 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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Name button will only be displayed
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Basic sequence editing The Sequence
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Duplicating a sequence You can dupl
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Figure 8-5 Sequence information win
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Figure 8-8 Sequence Editor with cod
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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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However, a Name Delimiter can also
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Figure 10-3 Advanced Expression for
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Once you have clicked on the AbN bu
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it is in the reverse orientation. T
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turn this option off, you make the
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You can use the Any Ambiguous Base
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Label Name Function I Ambiguities D
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• If there are two or more disagr
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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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You can also perform the deletion b
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match a high quality segment of seq
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. Page Intentionally Left Blank SEQ
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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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translations. Alternately, you can
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Note: Remember that even if a seque
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clicking any of the buttons to hide
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Table 15-1 Summary of Select comman
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When you are looking at a chromatog
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A dialog box (Figure 16-2) lets you
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Getting more information about an e
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You can now enter information in th
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The default setting shows exact mat
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Features What is a feature A featur
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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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Set the margins by typing appropria
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Colors as Backgrounds Sometimes, di
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Choosing a genetic code You will fi
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Layout. Select the submenu option c
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Figure 21-6 Confidence Ranges: sett
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Figure 21-9 Sound preference settin
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Figure 21-11 Chromatogram preferenc
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Figure 21-14 Contig preference sett
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Figure 21-16 Format ruler preferenc
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Figure 21-19 File import preference
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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 Mac Select Ne
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Menu/Window Command Mac 2 cutters C
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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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For a more detailed discussion of t
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Table 27-2 Feature Qualifiers Quali
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Feature Key Default Feature Qualifi
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Name CursorProject Window Dialog bo
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