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

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The default setting shows exact matches only. To show the reverse complement for a motif, click the Find Reverse Complement checkbox. Use the radio buttons to specify whether you want to highlight the motif using the exact bases you entered or using ambiguous matches. To specify how you would like the motif you are entering to be highlighted, click on the Display Style pull down menu (Figure 17-2) to choose color, case and underlining while the cursor is still blinking in the entry field. In the example (Figure 17-2), every instance of ‘AAAAA’ will be underlined and every start codon (ATG) will be shown in lower-case letters. You can save the motifs in a file on your hard disk by clicking on the Save Motifs button. Enter a suitable name for your motif file in the Save dialog window. Figure 17-2 Display style pull down menu Quick motif entry Select the bases in a Sequence Editor, then go to the Edit menu and click on Enter Selection As Motif. If you choose this command the default style will be used (see Chapter 21 “Customizing Sequencher and User Preferences”). Displaying motifs To use the motifs you have entered, go the View menu and choose Display Motifs. Figure 17-3 shows how motifs are displayed in the contig overview: they are the small downward facing colored blocks on the arrows representing the sequences. The colors are those you set in the Motif Default Style menu (see Chapter 21 “Customizing Sequencher and User Preferences”). SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 154
Figure 17-3 Overview showing motifs In the Bases view of a sequence motifs will appear highlighted in the manner you specified. You may need to deselect Display Color Bases, Colors As Backgrounds or Display Base Confidences to see the Motifs more clearly. In Figure 17-4, for example, all start codons are in lower case type and blue with only Colors as Backgrounds on. Figure 17-4 Sequence Editor showing motifs If you have a certain set of motifs you want to use for several projects (for example, if you use motif definitions to highlight certain restriction sites), you can save your definitions to a file. To do so, click Save Motifs at the top of the motifs window and follow the instructions. Then click the Load Motifs button to use those definitions in other projects. Features What is a feature A feature represents a subsequence or region of a sequence which has some biological significance. Assigning a feature is a method of describing and naming such a region. Sequencher supports both personal features and GenBank standardized features. The Feature Editor enables you to name and highlight sequence regions of special interest. Note: Features will not appear unless you go the View menu and select Display Features. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 155
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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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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
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Page 134 and 135: Figure 13-17 The Translated Varianc
Page 136 and 137: Figure 13-19 Extract from Variance
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Page 162 and 163: Figure 16-2 Restriction map options
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Page 166 and 167: Figure 16-8 Checkmarked enzyme list
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Page 172 and 173: Creating and editing features To cr
Page 174 and 175: Quick feature creation To create a
Page 178 and 179: Figure 18-1 A dimmed icon Finding t
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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
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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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