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

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Basic Reference Sequence properties When you assemble sequences, which include a Reference Sequence, the base numbering of a contig will be the same as the base numbering of the Reference Sequence (see Figure 7-1). Figure 7-1 Contig showing base numbering set by Reference Sequence When a contig is built that includes a Reference Sequence, the contig will always remain in the same orientation relative to that Reference. This way you can keep the contig from flipping as more fragments are added. Because of this, there can only be one Reference Sequence in a contig. You can easily spot the Reference Sequence in a contig editor because it is highlighted along its entire length with a gray border. When you assemble sequences that include a Reference Sequence you will notice that gaps in the Reference Sequence are given decimal numbers, thereby preserving the absolute numbering of base positions. The Reference Sequence does not contribute to the calculation of the consensus line of a contig. For example, if a ‘T’ in the Reference Sequence overlaps a ‘G’ in another fragment, the consensus line will show a ‘G’. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 44
Figure 7-2 Base numbering showing decimal numbers Working with a Reference Sequence How to mark a sequence as a Reference To designate a sequence as a Reference Sequence, select the sequence icon in the Project Window and under the Sequence menu select the Reference Sequence command. From now on, that sequence icon will include a small letter “R” to remind you that it has been marked as a Reference. Assemble to Reference Assemble to Reference is a powerful command which allows you to assemble all the samples you select to a single Reference Sequence, regardless of any inconsistencies between the individual fragments. Because it is a many-to-one comparison instead of the normal many-to-many comparison, Assemble to Reference is much faster than the standard Assemble Automatically mode. To Assemble to Reference, select the sequence fragments you want to assemble. Click the Assemble to Reference button or go to the Contig menu and choose the Assemble Contigs command, then click on Assemble to Reference. You will get a warning dialog box if you have not included a properly designated Reference Sequence among your selected sequences. Note that you use the Assembly Parameters to change the conditions under which the assembly will take place. (See Chapter 9 “Sequence Assembly” for more information.) To Reference by Name To Reference by Name is a special case where the behavior of the Reference Sequence is modified to work with the Assemble by Name command. The To Reference by Name button will only be displayed if Assemble by Name has been enabled. (For more information on Assemble by Name see Chapter 9 “Sequence Assembly”.) SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 45
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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 ..........
Page 10 and 11: 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
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
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
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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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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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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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