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

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You may require a more complex delimiter then those provided in the Name Delimiters drop down menu. You can use regular expressions to define these more complex delimiters. Table 24-1 Examples of delimeter expressions # Delimiter Sequence Name Handle 1 Handle 2 Handle 3 Handle 4 Handle 5 Handle 6 Expression 1 % Gel%A%T7%dog Gel A T7 dog 2 \ Gel%A%T7%dog Gel %A%T7 %dog 3 \% Gel%A%T7%dog Gel A%T7 dog 4 \I% Gel%A%T7%dog Gel A T7 dog If your sequence name is complex you may need to write a regular expression that describes the delimiters and the Assembly Handles. In the example below the text between the parentheses defines the Assembly Handles. Anything not enclosed by parentheses will be treated as a delimiter. (Assembly Handle 1)Delimiter(Assembly Handle 2)Delimiter(Assembly Handle 3) You would use this kind of expression with the Expression is a delimiter box unchecked. Regular expressions are powerful tools. There are many resources on the internet which describe how to use regular expressions. Here is one to help you get started. http://www.macadamian.com/column/regular_expressions.html SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 206
25. Appendix - IUPAC-IUB Standard Code Code Base(s) Meaning A A Adenine C C Cytosine G G Guanine T T Thymine U U Uracil (RNA) R A or G Purine Y C or T (or U) Pyrimidine K G or T (or U) Keto M A or C Amino S G or C Strong W A or T (or U) Weak 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 A, C, G, T (or U) (Any) SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 207
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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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Page Intentionally Left Blank xv
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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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Page Intentionally Left Blank SEQUE
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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
Page 172 and 173: 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
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Page 186 and 187: Figure 19-1 Export Options dialog b
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Page 190 and 191: Figure 19-3 Copy As Protein Transla
Page 192 and 193: [Project Name] and [User Name]. You
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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
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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
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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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