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Appendix B
B.1
Appendix B: AlphaEaseFC Molecular
Weight Library Files
A library including the following DNA, RNA and protein molecular weight standards has been
incorporated into AlphaEaseFC. For information about using these standard files, see Section
5.2.
DNA Size Standards (in bp)
HINDIII PHIX174 BRL10BP BRL50BP BRL100BP PRO100BP BRL123BP BRL1KB BRLHIMW
23130 1353 200 500 1500 1500 4182 12216 48502
9416 1078 190 450 1400 1000 4059 11198 38416
6557 872 180 400 1300 900 3936 10180 33498
4361 603 170 350 1200 800 3813 9162 29942
2322 310 160 300 1100 700 3690 8144 24776
2027 281 150 250 1000 600 3567 7126 22621
564 271 140 200 900 500 3444 6108 19399
125 234 130 150 800 400 3321 5090 17057
194 120 100 700 300 3198 4072 15004
118 110 50 600 200 3075 3054 12220
72 100 500 100 2952 2036 10086
90 400 2829 1636 8612
80 300 2706 1018 8271
70 200 2583 517
60 100 2460 396
50 2337 344
40 2214 298
30 2091 220
20 1968 201
10 1845 154
1722 134
1599 75
1476
1353
1230
1107
984
861
738
615
492
369
246
123
- AlphaImager™ IS-2200 1
- For Windows 2000/XP 1
- AlphaImager 2
- 2200 – 2
- AlphaEaseFC User’s Manual 2
- 1.2.1 System Components 8
- 1.2.2 System Placement 8
- 1.2.3 Cable Connections 8
- 1.5 System Information 15
- 1.6 Acquiring an Image 16
- 1.6.1 Focusing on an Image 17
- Selecting a Filter 21
- Displays 23
- Imaging Functions 32
- 2.1 Contrast Adjustment 33
- Black Level Adjustment 34
- White Level Adjustment 35
- Gamma Setting Adjustment 35
- The Auto Contrast Selection 36
- The Reverse Button 37
- The Grid Button 37
- 2.2 Tool Bar 40
- Sample Printouts 42
- 2.3 Tool Box 43
- 2.4 Status Bar 43
- Chapter 3: Drop Down Menus 46
- File Open 47
- File Overlay 48
- File Close 48
- File Save and Save As 49
- File Types: 50
- Chapter 3: Drop Down Menus 52
- 3.2 The Edit Menu 53
- Reset and Clear 54
- 3.3 The Image Menu 55
- Conversion 56
- Flat Field Calibrate 57
- 3.4 The Setup Menu 59
- Load Defaults 60
- Preferences 63
- 3.5 The Overlay Menu 66
- 3.6 The Utilities Menu 69
- Notepad 70
- 3.7 The View Menu 71
- Zoom Functions 72
- Show Annotations 72
- 3.8 The Help Menu 73
- Chapter 4: The Image 76
- 4.2 The Rotate / Flip Tool 77
- 4.3 Histogram 78
- 4.4 Automatic Enhancement 79
- 4.5 Annotations 81
- Chapter 4: Enhancement Tools 82
- Text Background and Font 83
- Text Angles 84
- The Drawing Tools 84
- The Editing Tools 86
- 4.6 False Color 88
- Palettes 2 through 11 89
- 4.7 Image Filters 90
- Sharpening Filters 92
- 3-D (Contour) Filters 92
- Noise Filters 93
- Smoothing Filters 93
- Edge Filters 93
- Horizontal Edge Filter 93
- Vertical Edge Filter 94
- Custom Filter 94
- The UNDO Button 94
- Examples of Filter Results 94
- 4.8 Movie Mode 95
- Frame Stacking 98
- BLANK PAGE 100
- Tools in the Toolbox 102
- Setting up an ARRAY Template 103
- Aligning the Template 104
- Measuring Density 105
- The INVERT Box 106
- Outputting Data 106
- Output Dialog Box 107
- Introduction 108
- Chapter 5: Analysis Tools 110
- Manually Selecting Bands 111
- Automatic Band Finding 111
- Special Functions: 115
- Snap to Peak 115
- The INVERT Button 115
- Calculating R 116
- Values 116
- The Graph Tool 117
- Auto Grid 118
- Setting up the Lane Template 119
- Specifying the Scan Width 120
- Scanning the Image 121
- Graph Display 122
- The Active Graph 122
- The Data Window 123
- Peak Detection Algorithms 125
- Set parameters dialog box 129
- Reset Base 130
- Base Subtract 130
- Interpreting 1D-Multi Data 130
- V. Line 130
- 3-D View 131
- Smooth Data 131
- The Invert Button 132
- Overlaying Graphs 133
- 1D-Multi 134
- Band Scoring 139
- Outputting Quantitative Data 141
- Exporting Graphs 141
- Exiting 1D-Multi 142
- Auto Lane 142
- Black Bands or White Bands 142
- Sensitivity Adjustment Bar 143
- Area of Interest Drawing 143
- Output Data 146
- Baseline 147
- Options 147
- Editing Peak Boundaries 147
- Auto Lane Editing Features 148
- Manual Band Matching 156
- Band Matching Results 157
- 5.4 Spot Density Tools 161
- Magic Wand and AutoSpot 163
- Magic Wand: 163
- Magic Wand Sensitivity 163
- Area of Interest 165
- Bright Spot vs Dark Spot 166
- Find Spots 166
- Background Threshold 166
- Moving Objects 168
- Deleting Objects 168
- Saving and Loading Objects 168
- Object Libraries 169
- Spot Density Measurements: 169
- Data Definitions 170
- Inverting the Data 170
- No Background 171
- Automatic Background 171
- Manual Background 172
- The Standard Curve Toolbox 173
- Displaying the Curve 175
- Outputting Quantitation Data 176
- Manual Count Tools 177
- Auto Count Tools 177
- Manual Count 179
- Automatic Count 180
- Editing Tools 182
- Displaying Spots 183
- Using the ADD SPOT Tool 183
- Using the Erase Spot Tool 184
- Spot Count Data 184
- Outputting Auto Count Data 185
- 5.6 The Scoring Function 187
- Scoring the Sample 188
- 5.7 The Ruler Function 190
- Appendix A: Opening 192
- AlphaEaseFC Files 192
- Weight Library Files 194
- To Change the Security Setup 196
- Security Features Dialog Box 197
- Instructions 202
- Cabinet Setup 203
- Camera Installation 206
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