| 140 | | = Pre-defined Tracks = |
| 141 | | == Overview Track == |
| 142 | | |
| 143 | | [[Image(track_overview.png)]] |
| 144 | | |
| 145 | | This track shows the range of present displayed window in the total genome. In above image, for instance, the blue-colored viewpoint shows the range from 125kb to 145kb. Clicking on any position of this overview track moves the viewpoint the middle position. For example, when you click on around 100k positions, the viewpoint will move to 90k-110k. |
| 146 | | |
| 147 | | |
| 148 | | == Ruler and Zooming Tracks == |
| 149 | | |
| 150 | | [[Image(image029.jpg)]] |
| 151 | | |
| 152 | | [[Image(image030.jpg)]] |
| 153 | | |
| 154 | | 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. |
| 155 | | |
| 156 | | In addition to the effect of the ruler track, if you click any position on the zooming track then two times zoom will be happened. For example, it is same to click the central button on zoom track as the zoomin.png button on main screen. On the other hand, it is also same to clicking the rightmost end of the zooming track as click ff.png then click zoomin.png on main screen. This track is useful to zoom out our interested region on the sequence.. |
| 157 | | |
| 158 | | |
| 159 | | == Base Color Track == |
| 160 | | |
| 161 | | [[Image(image032.jpg)]] |
| 162 | | |
| 163 | | [[Image(image033.jpg)]] |
| 164 | | |
| 165 | | 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). |
| 166 | | |
| 167 | | It is also possible to customize the corresponding base pair color also. For example, if GC base pair are only colored then we can use it as a simple GC content track. To get the sequence itself, it is better to save from fasta track. |
| 168 | | |
| 169 | | |
| 170 | | == GC Content Track == |
| 171 | | |
| 172 | | [[Image(image035.jpg)]] |
| 173 | | |
| 174 | | This track displays the ratio of GC contents for 5 pixels. If the pixel number of a base pair is more than 5, the coloring will be done to tell whether it is GC or AT. |
| 175 | | |
| 176 | | |
| 177 | | == Mapped Gene Track == |
| 178 | | |
| 179 | | [[Image(image036.jpg)]] |
| 180 | | |
| 181 | | This track displays the mapping result of Fugu, Zebra fish and Medaka’s Est to the Medaka genome, done by ALPS (http://alps.gi.k.u-tokyo.ac.jp). The mapping region for the gene is displayed by line and the exons are shown in rectangular box. The arrow sign shows the plus or minus strand of the genome. The above image displays Medaka’s ESTs in black color, while the green color indicates cDNAs of Fugu. The current data sources of mapped genes are Medaka Unigene Build#10, Zebra fish Unigene Build#71, and Fugu ensemble pufferfish v21.2.c1( 10th May, 2004). We will revise the alignment periodically in response to the update of the data sources. |
| 182 | | |
| 183 | | == Predicted Gene Track == |
| 184 | | |
| 185 | | This track displays the medaka predicted genes as Mapped gene track. It is viewed on lines, where the exons parts are on rectangular shape. Arrow sign shows the plus or minus strand of the genome. |
| 186 | | |
| 187 | | == 5’SAGE track == |
| 188 | | This track displays the medaka expression profile by showing mapped 5’end tag of an expressed Gene. Details of each tag can be found by clicking on each viewed rectangle on this track. |
| 189 | | |
| 190 | | == Sequence quality track == |
| 191 | | This track presents the quality value of medaka assembled sequences. The quality value of a subsequence in a scaffold can be viewed by inserting sequence’s scaffold name and location on main window. |
| 192 | | |
| 193 | | == Coverage track == |
| 194 | | This track displays coverage ratio of a specific sequence from a scaffold, determined by aligning Plasmid read sequence on genome. |
| 195 | | |
| 196 | | == Fosmid End Track == |
| 197 | | This track displays all the mapped fosmid reads obtained at the National Institute of Genetics(NIG,Japan) by using rectangular box in a line. |
| 198 | | |
| 199 | | == Bac End Track == |
| 200 | | |
| 201 | | == RFLP marker Track == |
| 202 | | This track presents known Restriction Fragment Length Polymorphism (RFLP) marker downloaded from () and mapped to medaka genomic sequence. |
| 203 | | |
| 204 | | == Repeat Element Track == |
| 205 | | This track displays all the repeat elements in medaka genome fixed by repeatmasker (ref), RepBase(ref) and de novo repeat finding tool(ref). The repeat element’s region is displayed by a rectangular box. |
| 206 | | |
| 207 | | == HNI alignment Track == |
| 208 | | This track displays all the polymorphisms regions between medaka Hd-rR and HNI strain. |
| 209 | | |
| 210 | | == Ensembel Predicted gene Track == |
| 211 | | This track displays medaka genes predicted on Enembel(ref) pipe line. The gene region is displayed by line and the bac ends are shown in rectangular box. The arrow sign shows the plus or minus strand of the genome. |
| 212 | | |
| 213 | | == Homology Track == |
| 214 | | Homologues genes of medaka-human, medaka-zebrafish, medaka-tetraodon, medaka-fugu are displayed in different tracks. |
