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

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Figure 12-4 Fill Void dialog box Deleting bases from the 5’ or 3’ ends Although you may have automatically trimmed your sequences for poor quality data when you imported them (see Chapter 6 “Preparing your data for assembly”), you may still need to delete a few 5’ bases to correct any mistakes made during the amplification process. Select the bases you want to delete. If you are at the 5’ (left end) then click the Forward Delete key. Sequencher will delete those bases without moving the entire sequence to the left. Similarly, if you choose bases on the 3‘ (right) end use the Backspace key and Sequencher will automatically delete those bases without realigning your sequence. Note: When editing from the consensus line you do not have to worry about the bases shifting to the left and right. Inserting gaps or bases into a contig If you want to insert gaps, go to the Sequence menu and click on Insert Gaps & Move Bases then choose Right or Left from the submenu. You can also create gaps by selecting a number of bases equivalent to the gap size you want to create. Press the Tab key if you want the selected bases to move to the right. To move to the left, hold down the Alt key when you press Tab. The space created will be filled with gap marks (small colon marks) that will appear without disrupting the rest of your contig. Once your gaps are in place you can either type the bases you want into the gap using Overstrike When Editing mode or use the lasso and grabber tools to move existing bases into the new position. Making edits from the consensus line You can simultaneously edit all the bases in the column above the position you choose in the consensus line, instead of individually changing each one. To do this, select a base in the consensus line and enter the character that represents the edit you want to make in that column. If you currently have a base selected in a sequence fragment, go to the Select menu and choose Contig Column (Ctrl+K). SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 96
Any bases in the sequences above the contig column you select that do not match the character you type will be changed to match the character you type in the consensus line. Your edits will appear according to the preferences you set in the View menu. Generally this will be magenta and bold-text. You can also delete bases from the consensus line. You cannot use the Undo command to reverse this action if your contig contains a Reference Sequence. Figure 12-5 The base is changed Note: Remember that changing bases from the consensus line edits only the sequences, after which the consensus is recalculated and displayed. Your action does not change the consensus directly. Changes in the consensus result from matching sequences with each other and evaluating them according to the type of consensus calculation you have chosen (e.g. by plurality, inclusively, forensic). Further note that this type of editing does not change Reference Sequences. Split After Selection… You can split a sequence fragment into two pieces. Put the cursor where you want to split the sequence. Go to the Sequence menu and choose Split After Selection…. Sequencher will ask you if you want to split the sequence after the last currently selected base. Click on the Split button to proceed. Sequencher will then split the sequence in two and label the new fragments for you. You can also apply the Split After Selection… command to an entire contig by simply making your selection in the consensus sequence, and then choosing Split After Selection… from the Sequence menu. Auto Match Sometimes you may wish to edit a number of sequences simultaneously, perhaps to match a high quality segment of sequence. Sequencher allows you to perform this type of mass edit on a range of bases using the Auto Match command. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 97
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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
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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
Page 62 and 63: When the To Reference by Name comma
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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
Page 98 and 99: it is in the reverse orientation. T
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
Page 106 and 107: Consensus to Forensic Standards In
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 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
Page 122 and 123: (see Figure 13-5). It is possible f
Page 124 and 125: Figure 13-7 Translated Variance Tab
Page 126 and 127: If you want to restrict the Compari
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
Page 138 and 139: The Population Table lists the vari
Page 140 and 141: If you want to remove sample sequen
Page 142 and 143: Select Individual Variance Reports
Page 144 and 145: If you prefer to copy your Translat
Page 146 and 147: You can copy your Translated Varian
Page 148 and 149: Summary report display options Sequ
Page 150 and 151: Enabling the protein display To ena
Page 154 and 155: Note: Remember that even if a seque
Page 156 and 157: If you select the Contig Chromatogr
Page 158 and 159: Select command Table 15-1 Summary o
Page 160 and 161: 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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