| 232 | | == Genscan Track == |
| 233 | | [[Image(genescan.jpg)]] |
| 234 | | |
| 235 | | This track displays the predicted genes by Genscan. The predicted genes are viewed on lines, where the exons parts are on rectangular shape. Arrow sign presents the strand of the genes. The above image shows the predicted genes in pack style. |
| 236 | | |
| 237 | | * Display settings |
| 238 | | |
| 239 | | If the cfg.png mark button on the left side of Genscan Track is clicked, the display setting will pop up. Here are the details of this setting. |
| 240 | | |
| 241 | | * Style selects setting |
| 242 | | |
| 243 | | Predicted genes’ display setting can be changed here. There are four kinds of display style. These styles are full, pack, small and dense, and they are similar to those styles in Mapped Gene Track. |
| 244 | | |
| 245 | | * Linkage of each gene |
| 246 | | |
| 247 | | In full, pack and small style each gene can be clicked on. After clicking each gene, the details of prediction by Genscan will be appeared. |
| 248 | | |
| 249 | | |
| 250 | | == Comparative Genomics Track == |
| 251 | | |
| 252 | | [[Image(comp.jpg)]] |
| 253 | | |
| 254 | | * Fugu Scaffold track |
| 255 | | |
| 256 | | * Description |
| 257 | | |
| 258 | | This track shows Fugu/Medaka homologous scaffolds detected by ALPS alignment program. Fugu scaffolds are denoted by boxes connected by arrows. The boxes represent regions of high homology (match ratio > 60%) aligned by ALPS. The arrows represent low homology regions or gaps in Fugu scaffold. The direction of arrows indicates the orientation of Fugu/Medaka alignments. Clicking on a Fugu scaffold will open a new window to display its dotplot with Fugu scaffold sequence provided in the same page. The Fugu sequence (Fugu v.2.0) was downloaded from JGI. |
| 259 | | |
| 260 | | * Method |
| 261 | | |
| 262 | | Fugu scaffold sequences are split into non-overlapping 300mer sequences and these 300mer sequences are mapped to Medaka scaffolds with ALPS. ALPS alignments with match ratio less than 60% are discarded and remaining alignments are chained by longest monotone subsequence algorithm. Chains consist of more than 10 alignments are displayed in the track. Note that inversions or microrearrangements are not shown. Only the longest monotone subsequence is displayed for each Fugu scaffold. |
| 263 | | |
| 264 | | * Linkage of each scaffold |
| 265 | | |
| 266 | | In full, pack and small style each gene can be clicked on. After clicking each scaffold, the detailed alignments will be appeared as like dot plot. Dotplot shows homologous regions of Fugu/Medaka scaffolds as diagonal runs of dots. Each dot, plotted based on sequence similarity score, indicates that significantly many seed matches are found between corresponding regions. The sequence similarity score is defined in such a way that tandem repeats are not assigned high scores while unique sequences are assigned high scores. |
| 267 | | |
| 268 | | |
