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

More documents

Recommendations

Info

consensus is from a base with a low confidence score. This type of base will be marked with a + (plus) or a • (bullet) below the consensus line. Each time you press Ctrl+N Sequencher moves the cursor to the next ambiguity in the consensus, starting after the currently selected character. After establishing this function, you can move to the next ambiguous base by hitting the spacebar or going to the Select menu and using the Repeat Select command. If you use the Shift key in conjunction with a Next Ambiguous Base key combination, the cursor will move in the reverse direction. Finding Disagreeing Bases You can find disagreeing bases quickly by typing Ctrl+D or clicking in the contig line, going to the Select menu and choosing Next Contig Disagree. This type of base will be marked with a • (bullet) below the consensus line Sequencher moves the cursor to the next disagreement in the consensus, starting after the currently selected character and ignoring ambiguities. Finding Low Confidence Bases You can quickly locate low confidence bases by typing Ctrl+L or by going to the Select menu and choosing Select Next Low Confidence Base. You can set the ranges for Low, Medium and High confidence in the User Preferences (see Chapter 21 “Customizing Sequencher and User Preferences”). Note: You can use the Next Low Confidence Base command to help direct your editing. Under the Window menu click on User Preferences… and set the Low Confidence range appropriately for the value range you wish to find. Go to the Select menu and click on Next Low Confidence Base to move your cursor directly to the bases that require attention. Finding Edited Bases You can quickly review edits already made to a contig by typing Ctrl+E or by going to the Select menu and choosing Next Edited Base. Note: This function will not find deletions. Performing edits The Edit Command To edit a base, first set the Edit mode you wish to use, then select the base by clicking on it (see Figure 12-1). Now type the new character over the old. If you accidentally type the wrong character, go to the Edit menu and choose Undo or just type over the mistake. Sequencher will recalculate the consensus line automatically. If you resolve an ambiguity at a particular position, the ambiguity marker below the consensus line disappears (see Figure 12-1). SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 92
Figure 12-1 A base is selected in the contig editor Editing modes The Edit command allows you to replace/overstrike, insert or erase a base call. The specific option you choose from the Edit menu will create that behavior. When you use Replace When Editing, the base you have just edited will remain highlighted. When you use Overstrike When Editing, the cursor will move one base to the right and this base will then be highlighted. Insert When Editing allows you to insert bases before the currently selected base, pushing all of the following bases forward. This also allows you to add bases beyond the end of a sequence. Sequencher uses Replace When Editing as its default setting. Note: If you insert or delete a base from any one sequence, the sequence may no longer align with other sequences after the point where you made your change. The consensus line will reflect this by showing lots of ambiguities in the form of bullets •. If you have made only one change, go to the Edit menu and the Undo command will remove it. Viewing Base Edits To assess the quality of your data, you need to be able to see how much modification has already been done to your contig as you edit it. When a base is edited, Sequencher changes its appearance by displaying it in magenta and bold-faced text. If you want edits to stand out even more (for instance in a black and white printout), you can also invert the case of the characters (e.g. change all edits from uppercase to lowercase text). To see the options for displaying edits, go to the View menu and click on the Base Edits As… submenu to choose from Not Highlighted, Bold Magenta, or bOLD and cASE cHANGE. Collect Gaps The Collect Gaps command allows you to select a range in a fragment or contig consensus and move all of the gaps within this selection to either the 5’ or the 3’ end of the selection. If you wish to collect the gaps within a single fragment, you must select the range within that fragment. Go to the Sequence menu and choose the Collect Gaps command. To SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 93
Page 2 and 3:
THIS IS AN AGREEMENT BETWEEN YOU, T
Page 4 and 5:
© 1991 - 2007 Gene Codes Corporati
Page 6 and 7:
Templates .........................
Page 8 and 9:
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
Page 16 and 17:
Page Intentionally Left Blank xv
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
Page 24 and 25:
Page Intentionally Left Blank SEQUE
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 34 and 35:
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 58 and 59: Page Intentionally Left Blank SEQUE
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
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 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
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
Page 162 and 163:
Figure 16-2 Restriction map options
Page 164 and 165:
example, if you were displaying onl
Page 166 and 167:
Figure 16-8 Checkmarked enzyme list
Page 168 and 169:
display this view by going to the V
Page 170 and 171:
The default setting shows exact mat
Page 172 and 173:
Creating and editing features To cr
Page 174 and 175:
Quick feature creation To create a
Page 176 and 177:
Page 178 and 179:
Figure 18-1 A dimmed icon Finding t
Page 180 and 181:
Note: If you pause between characte
Page 182 and 183:
a dialog box (Figure 18-6). This le
Page 184 and 185:
Page 186 and 187:
Figure 19-1 Export Options dialog b
Page 188 and 189:
You should remember to provide a re
Page 190 and 191:
Figure 19-3 Copy As Protein Transla
Page 192 and 193:
[Project Name] and [User Name]. You
Page 194 and 195:
Page 196 and 197:
Colors as Backgrounds Sometimes, di
Page 198 and 199:
Choosing a genetic code You will fi
Page 200 and 201:
time you select the Review button f
Page 202 and 203:
Label & Name The Label & Name prefe
Page 204 and 205:
Click the Use Blank Project radio b
Page 206 and 207:
Use the Columns For Multiple Traces
Page 208 and 209:
If you are making changes to the wa
Page 210 and 211:
Variance Table The Variance Table p
Page 212 and 213:
Page 214 and 215:
Figure 22-1 The Validate mtDNA Prof
Page 216 and 217:
Figure 22-3 The Circular Genome Siz
Page 218 and 219:
Page 220 and 221:
Menu/Window Command Windows Select
Page 222 and 223:
You may require a more complex deli
Page 224 and 225:
Page 226 and 227:
Code Base(s) Meaning 5 A or Another
Page 228 and 229:
Feature Display Color Style Second
Page 230 and 231:
Page 232 and 233:
eferences numbers, sequences, or us
Page 234 and 235:
Qualifier type Description Citation
Page 236 and 237:
Feature Key Default Feature Qualifi
Page 238 and 239:
Page 240 and 241:
Name CursorProject Window Dialog bo
show all

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

Create successful ePaper yourself

Delete template?

Save as template?