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

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Protein translations for the Consensus or Reference Sequence .............................................................. 134 Protein translations for Fragments .......................................................................................................... 134 Matching Proteins As Dashes.................................................................................................................. 134 Using the formatting ruler ....................................................................................................................... 135 Reverse and Complement a contig .......................................................................................................... 135 15. CHROMATOGRAMS ................................................................................ 137 Working with automated sequencer data ........................................................................ 137 Viewing chromatograms from a Sequence Editor .................................................................................. 137 Viewing chromatograms from a contig editor ........................................................................................ 138 Understanding the Trace Display ............................................................................................................ 139 Display secondary peak........................................................................................................................... 140 Select Next Commands ........................................................................................................................... 141 Editing bases from traces ........................................................................................................................ 142 Reverting to experimental data ............................................................................................................... 143 Reverting assembled sequences back to experimental data .................................................................... 143 Adjusting trace positions ......................................................................................................................... 144 16. RESTRICTION MAPS .............................................................................. 145 Displaying a Restriction Map.................................................................................................................. 145 Restriction Map display options ..................................................................................... 145 How to select enzymes ............................................................................................................................ 145 How to show cut positions or fragment sizes.......................................................................................... 146 How to set the map style ......................................................................................................................... 146 Setting the map width.............................................................................................................................. 147 Setting the map caption ........................................................................................................................... 147 Getting more information about an enzyme............................................................................................ 148 Changing the selected enzyme ................................................................................................................ 148 Changing the default enzymes ................................................................................................................ 150 Adding and editing enzymes ................................................................................................................... 150 Changing the recognition sequence ........................................................................................................ 151 Salt concentration effects ........................................................................................................................ 151 Saving new or modified enzymes ........................................................................................................... 151 Setting the sequence selection in a Sequence Editor .............................................................................. 151 Setting the sequence selection in a contig editor .................................................................................... 151 Copying the map ..................................................................................................................................... 152 17. MOTIFS AND FEATURES........................................................................ 153 Motifs .............................................................................................................................. 153 Entering motifs ........................................................................................................................................ 153 Quick motif entry .................................................................................................................................... 154 Displaying motifs .................................................................................................................................... 154 Features ........................................................................................................................... 155 What is a feature...................................................................................................................................... 155 Creating and editing features .................................................................................................................. 156 Editing an existing feature ...................................................................................................................... 156 Quick feature creation ............................................................................................................................. 158 xi
Showing and hiding features ................................................................................................................... 158 Listing a sequence’s features ................................................................................................................... 158 18. FINDING ITEMS ....................................................................................... 161 Finding the Project Window.................................................................................................................... 161 Finding open windows with menu commands ........................................................................................ 161 Finding open windows in the Project View ............................................................................................ 161 Finding the current selection ................................................................................................................... 162 Searching in Open Windows ........................................................................................... 162 Finding a subsequence ............................................................................................................................ 162 Refining a subsequence search ........................................................................................ 163 Exact matching ........................................................................................................................................ 163 Matching ambiguous bases ..................................................................................................................... 163 Any ambiguous match............................................................................................................................. 163 Finding bases by number ........................................................................................................................ 163 Extend Selection...................................................................................................................................... 163 Other search options ................................................................................................................................ 163 Project Window selection ............................................................................................... 163 Finding an item by name ......................................................................................................................... 163 Selecting all items that… ........................................................................................................................ 164 Contain a subsequence ............................................................................................................................ 165 Contain Items Named .............................................................................................................................. 165 Contain Items With Names Containing................................................................................................... 165 Have Chromatograms.............................................................................................................................. 166 Have Comments Containing… ............................................................................................................... 166 Have Labels Containing… ...................................................................................................................... 166 Have Names Containing… ..................................................................................................................... 167 Were Edited On Or Since… .................................................................................................................... 167 19. EXPORTING DATA .................................................................................. 169 Exporting data from Sequencher .................................................................................... 169 Exporting Sequences ............................................................................................................................... 169 Exporting a Consensus ............................................................................................................................ 170 Exporting Contigs ................................................................................................................................... 171 Exporting Selection as subproject ........................................................................................................... 171 Export Selected Bases ............................................................................................................................. 172 Export Options ........................................................................................................................................ 172 Export Formats ........................................................................................................................................ 172 Exporting protein translations ................................................................................................................. 173 Export Overviews.................................................................................................................................... 174 Exporting contig summaries ................................................................................................................... 174 20. OUTPUT ................................................................................................... 175 Copy picture ............................................................................................................................................ 175 Print setup................................................................................................................................................ 175 Print Trace in One Page........................................................................................................................... 175 Printing in detail ...................................................................................................................................... 175 xii
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 10 and 11: The Bases View ....................
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
Page 60 and 61: 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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