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

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When the To Reference by Name command is used, each contig created will contain a Reference Sequence and will also retain the numbering of the Reference Sequence. To use To Reference by Name, select the sequence fragments and Reference Sequence you want to assemble. Click the To Reference by Name button or go to the Contig menu and choose the Assemble Contigs command and then click onto Reference by Name from the submenu. Trim to Reference The Trim to Reference Sequence command is used to remove bases in a contig that flank the Reference Sequence on both the 5’ and 3’ ends (see Figure 7-3). To use this command, go to the Contig menu and choose Trim to Reference Sequence. This command is only available when you are in a contig that contains a Reference Sequence. Note: You cannot undo this action. If there are any sequences, which do not overlap the Reference Sequence they will be removed from the contig. Sequencher will warn you which fragments have been removed in a window, which you can print for your records. Figure 7-3 Contig with Reference Sequence flanked by overhanging sequence (before and after) Contig Editing with a Reference Sequence If you try to edit a Reference Sequence which has been assembled into a contig using either the standard Assemble Automatically or Assemble to Reference, a warning dialog will be displayed asking if you are sure this is what you want to do. You can proceed with the edit by clicking the Yes button. You can cancel the warning and continue to edit by clicking the No button. The Reference Sequence is protected from any changes you make while you are editing in the consensus line. Therefore, if you delete gaps from the consensus this will not affect the Reference Sequence unless it also has gaps at the position of the deleted bases. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 46
For example, you can delete a range of bases from all fragments by selecting a range within the Consensus sequence. When the deleted bases are in the middle of a fragment they will be replaced with gaps to maintain the alignment with the Reference Sequence. Since the action cannot be reverted using the Undo command, you must use the Revert to Experimental Data command from the Sequence menu to recover. Fill Coverage Gaps with Reference Under normal circumstances the Reference Sequence does not contribute to the calculation of the consensus. However, there is a special instance where the only data available in a particular region may be the data in the Reference Sequence. This might happen if you have aligned cDNAs to a genomic reference. The command Fill Coverage Gaps with Reference from the Contig menu will allow you to fill the gap with bases from the Reference Sequence. The bases from the Reference Sequence are dropped into the consensus line, but only in those places where there is no other data (Figure 7-4). Figure 7-4 Filling gaps with the Reference Sequence Reference Sequence Translation This command is only available when the Reference Sequence is assembled into a contig. To see a translation of the Reference Sequence in the notation line below the consensus sequence, go to the View menu and choose Reference Sequence Translation. The translation has a pale gray border above and below the amino acids to distinguish it from the consensus sequence translation. Note: As you cycle through the Consensus translation button modes, you will notice one mode which translates the consensus sequence in the same frame as the Reference Sequence. In this mode, the button icon is marked with an “r”. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 47
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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 ....................
Page 12 and 13: Protein translations for the Consen
Page 14 and 15: Setting header, footer and margin o
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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
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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
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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
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
Page 90 and 91: When you use a Name Delimiter, it w
Page 92 and 93: If the Expression is a delimiter bo
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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Figure 12-4 Fill Void dialog box De
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First select the base or range of b
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Page Intentionally Left Blank SEQUE
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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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