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

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When you use a Name Delimiter, it will look like this: or handle1-handle2-handle3 handle1_handle2_handle3. However, a Name Delimiter can also be a combination of letters, numbers and characters. To define your Name Delimiter, Sequencher provides a set of commonly used characters as a drop down menu in the Assemble by Name Settings dialog. You will see this menu if you go to Assembly Parameters and click on the Name Settings… button. When your naming convention does not use simple characters as Name Delimiters, you can use formal descriptors known as “regular expressions” instead, which we describe later in this chapter. Once you have defined an Assembly Handle, you will be able to assemble all of the sequences in your project. Only sequences that share the same Assembly Handle will be analyzed for assembly into the same contig. In a clinical application, for example, several contigs might be created with each contig representing sequence data from only a single patient, provided that each sample (patient) has a unique Assembly Handle in its name. Setting the Assemble by Name Conditions Configuring Assembly Handles using a Single Delimiter Starting in the Project Window, click on the Assembly Parameters button. At the bottom of the Assembly Parameters window, click on the Name Settings… button. The Assemble by Name Settings window appears in Figure 10-1 below. Figure 10-1 Assemble by Names Settings window SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 74
If your Assembly Handles are separated by a single character included in the Name Delimiters drop down menu, choose that character from the list. Otherwise, follow the directions for an Advanced Expression. Figure 10-2 The Name Delimiters drop down menu Configuring Assembly Handles using Advanced Expressions You will need to create an Assembly Handle using a regular expression if your Assembly Handle is not separated by one of the characters in the Name Delimiters drop down menu. What is a regular expression A regular expression is a way of describing a text pattern using letters, numbers, and special characters. These expressions follow certain syntactical rules. Starting in the Project Window, click on the Assembly Parameters button. At the bottom of the Assembly Parameters window, click on the Name Settings… button. The Assemble by Name Settings window appears. Choose Advanced Expression… from the Name Delimiters drop down menu. You will notice that the Define… button is now enabled. Click on the Define… button. The Advanced Expression for Name Parsing window appears. At the top of the window is a text box where you can type in a regular expression. Assemble by Name uses regular expressions in two ways. When the Expression is a delimiter box is checked, the regular expression you type in lets you define a delimiter option other than one available from the drop down menu. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 75
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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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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
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 60 and 61: Basic Reference Sequence properties
Page 62 and 63: When the To Reference by Name comma
Page 66 and 67: A locked editor is read-only. You c
Page 68 and 69: If your sequence was called “MyPU
Page 70 and 71: Viewing summary information in the
Page 72 and 73: Figure 8-7 ORF selected by Next Met
Page 74 and 75: If you want to assign a personal an
Page 76 and 77: Voice verification Sequencher provi
Page 80 and 81: Chapter 9 “Sequence Assembly” f
Page 82 and 83: Figure 9-2 The Clean Data algorithm
Page 84 and 85: Performing the assembly Automatic a
Page 86 and 87: Figure 9-5 Interactive assembly sho
Page 88 and 89: The new contig will appear in the P
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Page 94 and 95: Figure 10-6 The Project Window with
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Page 100 and 101: Figure 11-2 Contig overview Fifure
Page 102 and 103: Base Numbers At Transitions Clickin
Page 104 and 105: Label Name Function E F G H Sequenc
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Page 108 and 109: consensus is from a base with a low
Page 110 and 111: move the gaps to the 5’ end, sele
Page 112 and 113: Figure 12-4 Fill Void dialog box De
Page 114 and 115: First select the base or range of b
Page 118 and 119: The Translated Variance Table If yo
Page 120 and 121: Structure of the Translated Varianc
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Page 124 and 125: Figure 13-7 Translated Variance Tab
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Page 128 and 129: Figure 13-13 Creating a Joined feat
Page 130 and 131: In either case, the method you choo
Page 132 and 133: You can edit your data directly in
Page 134 and 135: Figure 13-17 The Translated Varianc
Page 136 and 137: Figure 13-19 Extract from Variance
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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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