Changes between Version 10 and Version 11 of UTGBManual
- Timestamp:
- 08/15/07 16:09:50 (18 years ago)
Legend:
- Unmodified
- Added
- Removed
- Modified
-
UTGBManual
v10 v11 2 2 3 3 [[PageOutline]] 4 5 == Welcome ==6 4 7 5 Welcome to UT Genome Browser (University of Tokyo Genome Browser). With this browser you can browse genomic information of a target species (at present Medaka only) from several aspects. For example, the following tasks can be performed with different combinations. … … 13 11 Questions, suggestions or comments are welcome to webmaster@utgenome.org. 14 12 15 = = Keyword Search ==13 = Keyword Search = 16 14 17 15 [[Image(keyword_top.png)]] … … 19 17 The top window displays the keyword search engine, as above picture illustrates. Inputting any keyword at the query box, we can see the detail information about the query. More about keyword search can be found in the help, written on the same window. In addition, if the keyword is a part of targets, then all the targets will be displayed. For example, the keyword “BCD” will match to “ABCD”, “BCDE”, “BCD” and “BCDF” etc. (this is worked out with using a suffix array.) 20 18 21 = == Gene List ===19 = Gene List = 22 20 23 21 [[Image(keyword_genes.png)]] … … 26 24 27 25 28 = == Mapping Position List ===26 = Mapping Position List = 29 27 30 28 [[Image(keyword_locs.png)]] … … 33 31 34 32 35 = = Sequence Alignment ==33 = Sequence Alignment = 36 34 37 35 [[Image(online01.PNG)]] … … 46 44 [[Image(online03.PNG)]] 47 45 48 = = Main Window ==46 = Main Window = 49 47 50 48 [[Image(browser_main.png)]] … … 60 58 In what follows, we describe the detail about each function. 61 59 62 == = Scrolling and zooming the main window ===60 == Scrolling and zooming the main window == 63 61 64 62 On main window, it is possible to shift and to zoom in/out the present observing sequence. These tasks can be carried out by: … … 89 87 90 88 91 == = Using shifting button method ===89 == Using shifting button method == 92 90 93 91 [[Image(browser_moves.png)]] … … 100 98 101 99 102 == = Using overview, ruler and zooming track method ===100 == Using overview, ruler and zooming track method == 103 101 104 102 In addition, there are some methods to shifting. These are overview, ruler, zooming trucks. You can shift the viewpoint by clicking any position of these tracks. For details, please refer to the respective details about the each track. 105 103 106 104 107 = = Functions of buttons ==105 = Functions of buttons = 108 106 109 107 (rev):: You can display the sequence in reverse mode by UT Genome Browser. Normally a sequence is displayed from left to right but you can reverse it with the (rev) button. An alternative way to display in reverse way is to input “start” value greater than “end” value in the Input Box. The same task can be done easily by clicking the (rev) button. As the (rev) button reverses start and end points of the present displayed sequence so this can change the display mode from normal to reverse or vice versa. If you press the (fasta) button on reverse mode, then the complementary strand of displayed strand will be retrieved. … … 131 129 132 130 133 == = Setting for Tracks ===131 == Setting for Tracks == 134 132 135 133 On main screen, when the cfg.png button, beside the track name, is pressed, the display of that track can be customized as above image. The customizing contents of the tracks differ from each other. On the other hand, there are some tracks which contents cannot be customized at all. For details, please refer to the individual tracks information. 136 134 137 135 138 = = Pre-defined Tracks ==139 == = Overview Track ===136 = Pre-defined Tracks = 137 == Overview Track == 140 138 141 139 [[Image(track_overview.png)]] … … 144 142 145 143 146 == = Ruler and Zooming Tracks ===144 == Ruler and Zooming Tracks == 147 145 148 146 Both the ruler track and the zooming track are displaying same contents with different color. These two show the base position number of the present displayed content with respect to the total sequence. If you click any position of the ruler track, the viewpoint will move to the middle position. For example, if the rightmost end of the ruler track is clicked then the same effect will be happed as the ff.png button of main screen is pressed. Before using the zoom button on main screen, it is better to have the required region on middle position by using the ruler track to smoothing future enlarge processing. … … 151 149 152 150 153 == = Base Color Track ===151 == Base Color Track == 154 152 155 153 Base color track changes the sequence to color mode. All four ATGC bases are displayed by converting to the individual color. It is natural to display each base pair by one pixel. By zooming in, you can see any specific region of the sequence in alphabet symbol (above bottom image).
