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

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Page Intentionally Left Blank SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 208
26. Appendix - Stanford Extended Code Code Base(s) Meaning A A Adenine C C Cytosine G G Guanine T T Thymine U U Uracil (RNA) P A or G Purine Q C or T (or U) Pyrimidine K G or T (or U) Keto J A or C M G or C L A or T (or U) B C, G, T (or U) not A D G, A, T (or U) not C H A, C, T (or U) not G V A, C, or G not T SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 209
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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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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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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
Page 174 and 175: Quick feature creation To create a
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Page 178 and 179: Figure 18-1 A dimmed icon Finding t
Page 180 and 181: Note: If you pause between characte
Page 182 and 183: a dialog box (Figure 18-6). This le
Page 186 and 187: Figure 19-1 Export Options dialog b
Page 188 and 189: You should remember to provide a re
Page 190 and 191: Figure 19-3 Copy As Protein Transla
Page 192 and 193: [Project Name] and [User Name]. You
Page 196 and 197: Colors as Backgrounds Sometimes, di
Page 198 and 199: Choosing a genetic code You will fi
Page 200 and 201: time you select the Review button f
Page 202 and 203: Label & Name The Label & Name prefe
Page 204 and 205: Click the Use Blank Project radio b
Page 206 and 207: Use the Columns For Multiple Traces
Page 208 and 209: If you are making changes to the wa
Page 210 and 211: Variance Table The Variance Table p
Page 214 and 215: Figure 22-1 The Validate mtDNA Prof
Page 216 and 217: Figure 22-3 The Circular Genome Siz
Page 220 and 221: Menu/Window Command Windows Select
Page 222 and 223: You may require a more complex deli
Page 226 and 227: Code Base(s) Meaning 5 A or Another
Page 228 and 229: Feature Display Color Style Second
Page 232 and 233: eferences numbers, sequences, or us
Page 234 and 235: Qualifier type Description Citation
Page 236 and 237: Feature Key Default Feature Qualifi
Page 240 and 241: Name CursorProject Window Dialog bo
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