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

More documents

Recommendations

Info

© 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved Sequencher is a trademark of Gene Codes Corporation Microsoft® is a registered trademark of Microsoft Corporation. Macintosh® is a trademark of Apple Computer, Inc. ABI, Applied Biosystems and 3730 are trademarks of Applied Biosystems, Inc. ALF is a trademark of Pharmacia Biotech. All other trademarks are the properties of their respective owners. iii
1. PREFACE ....................................................................................................... 1 Gene Codes ......................................................................................................................... 1 2. USING THIS MANUAL ................................................................................... 3 Conventions used in this manual ........................................................................................ 3 Installing Sequencher .......................................................................................................... 3 Sequencher Help ................................................................................................................. 3 Navigating Sequencher Help....................................................................................................................... 4 Context Sensitive Screens ........................................................................................................................... 4 The button bar ..................................................................................................................... 5 Sequencher’s menus ............................................................................................................ 5 Sequencher .................................................................................................................................................. 5 File menu ..................................................................................................................................................... 5 Edit menu .................................................................................................................................................... 5 Select menu ................................................................................................................................................. 5 Contig menu ................................................................................................................................................ 6 Sequence menu............................................................................................................................................ 6 View menu .................................................................................................................................................. 6 Window menu ............................................................................................................................................. 6 Help menu ................................................................................................................................................... 6 Context Sensitive menus and buttons ................................................................................. 6 Contextual menus ............................................................................................................... 6 Keyboard shortcuts ............................................................................................................. 7 3. THE PROJECT WINDOW .............................................................................. 9 Sequencher concepts ........................................................................................................... 9 About the Project Window .......................................................................................................................... 9 Creating a new project ................................................................................................................................ 9 Opening an existing project ...................................................................................................................... 10 Working with items in the Project Window .............................................................................................. 11 Icon types .................................................................................................................................................. 11 Project views ......................................................................................................................11 View as Large Icons .................................................................................................................................. 11 View as Small Icons .................................................................................................................................. 12 Moving icons ............................................................................................................................................. 12 Cleaning up ............................................................................................................................................... 12 View as a list ............................................................................................................................................. 13 Project Window Columns ......................................................................................................................... 13 Viewing constituent sequences ................................................................................................................. 15 Viewing the information for a sequence or contig .................................................................................... 15 Editing the information for a sequence or contig ...................................................................................... 16 The Project Window button bar ................................................................................................................ 16 iv
Page 2 and 3: THIS IS AN AGREEMENT BETWEEN YOU, T
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: 21. CUSTOMIZING SEQUENCHER AND USER
Page 16 and 17: Page Intentionally Left Blank
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: If you are working with ABI sequenc
Page 32 and 33: Figure 3-10 The Get Info window If
Page 34 and 35: Page Intentionally Left Blank SEQUE
Page 36 and 37: How to import using menu commands I
Page 38 and 39: Sequencher tells you how many files
Page 40 and 41: Double-clicking a project icon When
Page 42 and 43: Closing a project If you have finis
Page 44 and 45: Selecting sequences Selecting seque
Page 46 and 47: Renaming a sequence or contig Renam
Page 48 and 49: the close box. In either case, Sequ
Page 50 and 51: will be a checkbox at an end if it
Page 52 and 53: Figure 6-4 Bases view in Ends 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:
Name button will only be displayed
Page 64 and 65:
Page 66 and 67:
Basic sequence editing The Sequence
Page 68 and 69:
Duplicating a sequence You can dupl
Page 70 and 71:
Figure 8-5 Sequence information win
Page 72 and 73:
Figure 8-8 Sequence Editor with cod
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 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:
However, a Name Delimiter can also
Page 92 and 93:
Figure 10-3 Advanced Expression for
Page 94 and 95:
Once you have clicked on the AbN bu
Page 96 and 97:
Page 98 and 99:
it is in the reverse orientation. T
Page 100 and 101:
turn this option off, you make the
Page 102 and 103:
You can use the Any Ambiguous Base
Page 104 and 105:
Label Name Function I Ambiguities D
Page 106 and 107:
• If there are two or more disagr
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:
You can also perform the deletion b
Page 114 and 115:
match a high quality segment of seq
Page 116 and 117:
. Page Intentionally Left Blank SEQ
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:
translations. Alternately, you can
Page 152 and 153:
Page 154 and 155:
Note: Remember that even if a seque
Page 156 and 157:
clicking any of the buttons to hide
Page 158 and 159:
Table 15-1 Summary of Select comman
Page 160 and 161:
When you are looking at a chromatog
Page 162 and 163:
A dialog box (Figure 16-2) lets you
Page 164 and 165:
Getting more information about an e
Page 166 and 167:
You can now enter information in th
Page 168 and 169:
Page 170 and 171:
The default setting shows exact mat
Page 172 and 173:
Features What is a feature A featur
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:
Set the margins by typing appropria
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:
Layout. Select the submenu option c
Page 202 and 203:
Figure 21-6 Confidence Ranges: sett
Page 204 and 205:
Figure 21-9 Sound preference settin
Page 206 and 207:
Figure 21-11 Chromatogram preferenc
Page 208 and 209:
Figure 21-14 Contig preference sett
Page 210 and 211:
Figure 21-16 Format ruler preferenc
Page 212 and 213:
Figure 21-19 File import preference
Page 214 and 215:
Page 216 and 217:
Figure 22-1 The Validate mtDNA Prof
Page 218 and 219:
Figure 22-3 The Circular Genome Siz
Page 220 and 221:
Page 222 and 223:
Menu/Window Command Mac Select Ne
Page 224 and 225:
Menu/Window Command Mac 2 cutters C
Page 226 and 227:
You may require a more complex deli
Page 228 and 229:
Page 230 and 231:
Code Base(s) Meaning 5 A or Another
Page 232 and 233:
Feature Display Color Style Second
Page 234 and 235:
Page 236 and 237:
For a more detailed discussion of t
Page 238 and 239:
Table 27-2 Feature Qualifiers Quali
Page 240 and 241:
Feature Key Default Feature Qualifi
Page 242 and 243:
Page 244 and 245:
Name CursorProject Window Dialog bo
Page 246:
show all

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

Create successful ePaper yourself

Delete template?

Save as template?