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

More documents

Recommendations

Info

Navigating Sequencher Help The Sequencher Help window consists of three main parts. There is a button bar at the top of the window. There is also a navigation pane on the left side of the window and a content pane on the right side of the window. The button bar has Back and Forward icons which function like a web browser’s Back and Forward buttons. If you click the Home button you will return to the Welcome screen. You can also type keywords into the Search entry text box. The navigation pane displays a Table of Contents. Click on the relevant icon to display any subtopics. Click on a page link icon in the navigation pane to display the Sequencher Help article in the content pane. Some of these pages contain underlined hyperlinks to related topics in the manual and a hyperlink to the following topic in the Table of Contents. You can also get information on specific topics such as Assembly Parameters or the Sequence Editor from context sensitive screens. To search for a specific topic, type the topic name into the search field at the top right corner of the Help Viewer. When your search is complete, double click on an item to display it. Figure 2-1 The Sequencher Help dialog window Context Sensitive Screens Context sensitive screens provide easy links to information about the region of Sequencher you are currently using. If you have the Project Window displayed when SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 4
accessing Help, then the Project Window context page will appear. This will be the case for most of Sequencher’s major windows. If you see a flagged icon, this means you can click on a link to get further information. If you place the cursor over this icon, a Tool Tip with the title of the Help article will be displayed. The button bar The button bar contains buttons for frequently used commands. It appears just below the top of many windows (see Figure 2-2). Figure 2-2 The Project Window button bar On many Sequencher windows you can use the smaller left-hand button, which has an up arrow on it, to hide the button bar. Click on the button and the button bar will “hide” behind the title bar. When the button bar is hidden, you can still see the bottom of the left-hand button under the title bar. It will show a down-pointing arrowhead. Click on the arrowhead and the button bar will reappear. Sequencher’s menus Sequencher The Sequencher menu gives you information on the version of Sequencher you have, contact information for Gene Codes Corporation and Sequencher technical support, access to the User Preferences and the Quit Sequencher command. File menu The commands in the File menu let you open, close and save projects as well as import and export data. You can also open and close windows, specify page setups and print from the File menu. Edit menu The commands in the Edit menu let you cut, copy and paste selected data. You can also duplicate fragments, mark motifs, reposition sequences and choose your editing mode from the Edit menu. Select menu The commands in the Select menu cover a variety of items you might want to find and/or highlight to help you in your analysis. These commands use a wide variety of criteria to help you locate items from sequence fragments, subsequences and individual bases. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 5
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 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 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 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 78 and 79:
Page Intentionally Left Blank SEQUE
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 96 and 97:
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 112 and 113:
Figure 12-4 Fill Void dialog box De
Page 114 and 115:
First select the base or range of b
Page 116 and 117:
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 152 and 153:
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?