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| | 127 | </head> |
| | 128 | |
| | 129 | <body lang=JA link=blue vlink=purple style='text-justify-trim:punctuation'> |
| | 130 | |
| | 131 | <div class=Section1 style='layout-grid:18.0pt'> |
| | 132 | |
| | 133 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 134 | 24.0pt'> </span></h1> |
| | 135 | |
| | 136 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 137 | 24.0pt'> </span></h1> |
| | 138 | |
| | 139 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 140 | 36.0pt'>UT Genome Browser</span></h1> |
| | 141 | |
| | 142 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 143 | 36.0pt'> </span></h1> |
| | 144 | |
| | 145 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 146 | 36.0pt'>User’s Manual</span></h1> |
| | 147 | |
| | 148 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 149 | 36.0pt'>Version 1.0</span></h1> |
| | 150 | |
| | 151 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 152 | 24.0pt'> </span></h1> |
| | 153 | |
| | 154 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 155 | |
| | 156 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 157 | |
| | 158 | <p class=MsoNormal align=center style='text-align:center'><b><span |
| | 159 | lang=EN-US style='font-size:24.0pt'>August 17, 2004</span></b></p> |
| | 160 | |
| | 161 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 162 | 24.0pt'> </span></h1> |
| | 163 | |
| | 164 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 165 | |
| | 166 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 167 | |
| | 168 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 169 | 22.0pt'>UT Genome Browser Development Team</span></h1> |
| | 170 | |
| | 171 | <h1 align=center style='text-align:center'><span lang=EN-US style='font-size: |
| | 172 | 22.0pt'> </span></h1> |
| | 173 | |
| | 174 | <b><span lang=EN-US style='font-size:18.0pt;font-family:Century'><br clear=all |
| | 175 | style='page-break-before:always'> |
| | 176 | </span></b> |
| | 177 | |
| | 178 | <h1><span lang=EN-US>Table of Contents</span></h1> |
| | 179 | |
| | 180 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 181 | |
| | 182 | <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height: |
| | 183 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>1<span |
| | 184 | style='font:7.0pt "Times New Roman"'> |
| | 185 | </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Welcome</span></b></p> |
| | 186 | |
| | 187 | <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height: |
| | 188 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2<span |
| | 189 | style='font:7.0pt "Times New Roman"'> |
| | 190 | </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Keyword |
| | 191 | Search</span></b></p> |
| | 192 | |
| | 193 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 194 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2.1<span |
| | 195 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 196 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Gene List</span></b></p> |
| | 197 | |
| | 198 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 199 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2.2<span |
| | 200 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 201 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Mapping Position List</span></b></p> |
| | 202 | |
| | 203 | <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height: |
| | 204 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>3<span |
| | 205 | style='font:7.0pt "Times New Roman"'> |
| | 206 | </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Online |
| | 207 | Sequence Alignment</span></b></p> |
| | 208 | |
| | 209 | <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height: |
| | 210 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4<span |
| | 211 | style='font:7.0pt "Times New Roman"'> |
| | 212 | |
| | 213 | </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Main |
| | 214 | Window</span></b></p> |
| | 215 | |
| | 216 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 217 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.1<span |
| | 218 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 219 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Scrolling and Zooming the |
| | 220 | Main Window</span></b></p> |
| | 221 | |
| | 222 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 223 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.2<span |
| | 224 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 225 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Functions of Buttons</span></b></p> |
| | 226 | |
| | 227 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 228 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.3<span |
| | 229 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 230 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Addition, Deletion, and |
| | 231 | Rearrangement of Tracks</span></b></p> |
| | 232 | |
| | 233 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 234 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.4<span |
| | 235 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 236 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Setting for Tracks</span></b></p> |
| | 237 | |
| | 238 | <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height: |
| | 239 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5<span |
| | 240 | style='font:7.0pt "Times New Roman"'> |
| | 241 | </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Pre-defined |
| | 242 | Tracks</span></b></p> |
| | 243 | |
| | 244 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 245 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.1<span |
| | 246 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 247 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Overview Tracks</span></b></p> |
| | 248 | |
| | 249 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 250 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.2<span |
| | 251 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 252 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Ruler and Zooming Tracks</span></b></p> |
| | 253 | |
| | 254 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 255 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.3<span |
| | 256 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 257 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Base Color Track</span></b></p> |
| | 258 | |
| | 259 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 260 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.4<span |
| | 261 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 262 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Gap Track</span></b></p> |
| | 263 | |
| | 264 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 265 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.5<span |
| | 266 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 267 | lang=EN-US style='font-size:14.0pt;line-height:150%'>GC Content Track</span></b></p> |
| | 268 | |
| | 269 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 270 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.6<span |
| | 271 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 272 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Mapped Gene Track</span></b></p> |
| | 273 | |
| | 274 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 275 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.7<span |
| | 276 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 277 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Genscan Track</span></b></p> |
| | 278 | |
| | 279 | <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height: |
| | 280 | 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.8<span |
| | 281 | style='font:7.0pt "Times New Roman"'> </span></span></b><b><span |
| | 282 | lang=EN-US style='font-size:14.0pt;line-height:150%'>Comparative Genomics Track</span></b></p> |
| | 283 | |
| | 284 | <p class=MsoNormal style='line-height:150%'><b><span lang=EN-US |
| | 285 | style='font-size:14.0pt;line-height:150%'>Ramen Assembler / UT Genome Browser |
| | 286 | Team Members</span></b></p> |
| | 287 | |
| | 288 | <p class=MsoNormal style='line-height:150%'><b><span lang=EN-US |
| | 289 | style='font-size:14.0pt;line-height:150%'>Acknowledgements</span></b></p> |
| | 290 | |
| | 291 | <span lang=EN-US style='font-size:10.5pt;line-height:150%;font-family:Century'><br |
| | 292 | clear=all style='page-break-before:always'> |
| | 293 | </span> |
| | 294 | |
| | 295 | <p class=MsoNormal style='line-height:150%'><span class=a><span lang=EN-US |
| | 296 | style='font-size:18.0pt;line-height:150%'>1. Welcome</span></span></p> |
| | 297 | |
| | 298 | <p class=MsoNormal><span lang=EN-US>Welcome to UT Genome Browser (University of Tokyo Genome Browser). With this browser you can browse genomic information |
| | 299 | of a target species (at present Medaka only) from several aspects. For example, |
| | 300 | the following tasks can be performed with different combinations. </span></p> |
| | 301 | |
| | 302 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 303 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 304 | </span></span><span lang=EN-US>You can search gene, by gene name, clone name, |
| | 305 | cluster name and display its surroundings gene groups.</span></p> |
| | 306 | |
| | 307 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 308 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 309 | </span></span><span lang=EN-US>You can map a genomic sequence to any genome and |
| | 310 | observe its surroundings.</span></p> |
| | 311 | |
| | 312 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 313 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 314 | </span></span><span lang=EN-US>You can save the sequence itself on your system |
| | 315 | from here.</span></p> |
| | 316 | |
| | 317 | <p class=MsoNormal><span lang=EN-US>Questions, suggestions or comments are |
| | 318 | welcome to <a href="mailto:webmaster@utgenome.org">webmaster@utgenome.org</a>.</span></p> |
| | 319 | |
| | 320 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 321 | |
| | 322 | <h1><span lang=EN-US>2. Keyword Search </span></h1> |
| | 323 | |
| | 324 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 325 | border=0 width=254 height=262 src="manual_e.files/image001.jpg" |
| | 326 | alt="keyword_top.png"></span></p> |
| | 327 | |
| | 328 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 329 | |
| | 330 | <p class=MsoNormal><span lang=EN-US>The top window displays the keyword search |
| | 331 | engine, as above picture illustrates. Inputting any keyword at the query box, we |
| | 332 | can see the detail information about the query. More about keyword search can |
| | 333 | be found in the help, written on the same window. In addition, if the keyword |
| | 334 | is a part of targets, then all the targets will be displayed. For example, the |
| | 335 | keyword “BCD” will match to “ABCD”, “BCDE”, “BCD” and “BCDF” etc. (this is |
| | 336 | worked out with using a suffix array.)</span></p> |
| | 337 | |
| | 338 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 339 | |
| | 340 | <h2><span lang=EN-US>2.1. Gene List</span></h2> |
| | 341 | |
| | 342 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 343 | border=0 width=288 height=235 src="manual_e.files/image002.jpg" |
| | 344 | alt="keyword_genes.png"></span></p> |
| | 345 | |
| | 346 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 347 | |
| | 348 | <p class=MsoNormal><span lang=EN-US>When there are many genes for one keyword |
| | 349 | search, all genes will be displayed on a list. Pressing the (*) button on the |
| | 350 | left side, you can go to the mapped region for the gene. This list appears when |
| | 351 | multiple candidate entries are found, typically when class names or part of a |
| | 352 | gene number are input as a keyword. If a Genebank accession number is given, |
| | 353 | the number must be unique, and hence this list does not appear. </span></p> |
| | 354 | |
| | 355 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 356 | |
| | 357 | <h2><span lang=EN-US>2.2. Mapping Position List</span></h2> |
| | 358 | |
| | 359 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 360 | border=0 width=384 height=230 src="manual_e.files/image003.jpg" |
| | 361 | alt="keyword_locs.png"></span></p> |
| | 362 | |
| | 363 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 364 | |
| | 365 | <p class=MsoNormal><span lang=EN-US>If the query gene has mapped to several |
| | 366 | regions on the genomic sequence, the list of all positions will be shown. Pressing |
| | 367 | the (*) button on the left side displays the mapped region of the gene. If |
| | 368 | there is only one mapped region of the gene, the list is skipped to display.</span></p> |
| | 369 | |
| | 370 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 371 | |
| | 372 | <h1><span lang=EN-US>3. Sequence Alignment </span></h1> |
| | 373 | |
| | 374 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 375 | border=0 width=408 height=195 src="manual_e.files/image004.jpg" |
| | 376 | alt=online01.PNG></span></p> |
| | 377 | |
| | 378 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 379 | |
| | 380 | <p class=MsoNormal><span lang=EN-US>Sequence mapping is possible by inputting a |
| | 381 | sequence in the online mapping frame (above image) at the bottom of the main |
| | 382 | window. After selecting the species and its revision, press the search button |
| | 383 | on the bottom. The request is sent to the alignment server ALPS to align the |
| | 384 | given sequence to the selected genome. Afterwards, the list of alignment |
| | 385 | results is returned if the system finds some alignments.</span></p> |
| | 386 | |
| | 387 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 388 | border=0 width=353 height=431 src="manual_e.files/image005.jpg"></span></p> |
| | 389 | |
| | 390 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 391 | |
| | 392 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 393 | border=0 width=400 height=81 src="manual_e.files/image006.jpg" |
| | 394 | alt=online02.PNG></span></p> |
| | 395 | |
| | 396 | <p class=MsoNormal><span lang=EN-US>From the list, you can select one alignment |
| | 397 | by clicking the result button as illustrated above. Then, the aligned result |
| | 398 | will appear on the browser. The ALPS mapping track in following snapshot |
| | 399 | displays the added mapping status.</span></p> |
| | 400 | |
| | 401 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 402 | |
| | 403 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 404 | border=0 width=566 height=149 src="manual_e.files/image007.jpg" |
| | 405 | alt=online03.PNG></span></p> |
| | 406 | |
| | 407 | <h1><span lang=EN-US>4. Main Window</span></h1> |
| | 408 | |
| | 409 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 410 | border=0 width=509 height=324 src="manual_e.files/image008.jpg" |
| | 411 | alt="browser_main.png"></span></p> |
| | 412 | |
| | 413 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 414 | |
| | 415 | <p class=MsoNormal><span lang=EN-US>The above picture shows the main screen for |
| | 416 | UT Genome Browser. It is possible to see the targeted region of genomic |
| | 417 | sequence by many tracks. This browser provides the following functions to |
| | 418 | manipulate tracks on this image screen.</span></p> |
| | 419 | |
| | 420 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 421 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 422 | </span></span><span lang=EN-US>Shifting, zooming in and out, and reversing of |
| | 423 | the target region. It facilitates zooming in the sequence until bases can be |
| | 424 | seen, while providing a panoramic, structural view for the sequence.</span></p> |
| | 425 | |
| | 426 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 427 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 428 | </span></span><span lang=EN-US>Adding, deleting and reordering the tracks.</span></p> |
| | 429 | |
| | 430 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 431 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 432 | </span></span><span lang=EN-US>Customizing of each track’s display.</span></p> |
| | 433 | |
| | 434 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 435 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 436 | </span></span><span lang=EN-US>Retrieving the present displayed sequence in Fasta |
| | 437 | format.</span></p> |
| | 438 | |
| | 439 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 440 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 441 | </span></span><span lang=EN-US>Continuing keyword search.</span></p> |
| | 442 | |
| | 443 | <p class=MsoNormal><span lang=EN-US>In what follows, we describe the detail |
| | 444 | about each function.</span></p> |
| | 445 | |
| | 446 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 447 | |
| | 448 | <h2><span lang=EN-US>4.1 Scrolling and zooming the main window </span></h2> |
| | 449 | |
| | 450 | <p class=MsoNormal><span lang=EN-US>On main window, it is possible to shift and |
| | 451 | to zoom in/out the present observing sequence. These tasks can be carried out |
| | 452 | by:</span></p> |
| | 453 | |
| | 454 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 455 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 456 | </span></span><span lang=EN-US>Inputting value in the input box method.</span></p> |
| | 457 | |
| | 458 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 459 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 460 | </span></span><span lang=EN-US>Using shifting button method.</span></p> |
| | 461 | |
| | 462 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 463 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 464 | </span></span><span lang=EN-US>Using overview, ruler and zooming track method.</span></p> |
| | 465 | |
| | 466 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 467 | |
| | 468 | <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Inputting |
| | 469 | value in the input box method</span></h3> |
| | 470 | |
| | 471 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 472 | border=0 width=552 height=31 src="manual_e.files/image009.jpg" |
| | 473 | alt="browser_params.png"></span></p> |
| | 474 | |
| | 475 | <p class=MsoNormal><span lang=EN-US>You can input values into the input boxes |
| | 476 | (like above image) inside the main window. The details about this method are as |
| | 477 | follows,</span></p> |
| | 478 | |
| | 479 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 480 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 481 | </span></span><b><span lang=EN-US>Species: </span></b><span lang=EN-US>Select |
| | 482 | the species to display. The selectable revisions would be changed with respect |
| | 483 | to the species. At present, only Medaka is possible to be selected.</span></p> |
| | 484 | |
| | 485 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 486 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 487 | </span></span><b><span lang=EN-US>Revision</span></b><span lang=EN-US>: Select |
| | 488 | the revision of the target specie’s genome. For Medaka, the revision name |
| | 489 | format is yyyymm. The selecting topics will change with respect to the selected |
| | 490 | revision.</span></p> |
| | 491 | |
| | 492 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 493 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 494 | </span></span><b><span lang=EN-US>Target: </span></b><span lang=EN-US>Select |
| | 495 | the target region to be displayed, from the selected species and selected |
| | 496 | revision. In the case of 200406 revision of Medaka, only scaffold name (e.g. |
| | 497 | scaffold123) can be selected but not the chromosome name (e.g. chr10). Chromosome |
| | 498 | numbers will be available in our later revision. </span></p> |
| | 499 | |
| | 500 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 501 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 502 | </span></span><b><span lang=EN-US>Start: </span></b><span lang=EN-US>Select the |
| | 503 | start position from your targeted sequence to display. The number should be 1-origin |
| | 504 | (i.e. the starting point will be 1).</span></p> |
| | 505 | |
| | 506 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 507 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 508 | |
| | 509 | </span></span><b><span lang=EN-US>End: </span></b><span lang=EN-US>Select the |
| | 510 | end point from your targeted sequence to display. The number should be 1-origin. |
| | 511 | If the ending point is greater than the starting point then the display will be |
| | 512 | normal. Otherwise, the display will be reverse. In both cases, the ending base |
| | 513 | will be included in the displaying sequence.</span></p> |
| | 514 | |
| | 515 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 516 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 517 | </span></span><b><span lang=EN-US>Width: </span></b><span lang=EN-US>Input the |
| | 518 | width in terms of pixels for output track display. Input the value that is |
| | 519 | suitable for your vision. Normally, it is assumed that width is equal to the |
| | 520 | screen width. It is also possible to input the width as 10 times bigger than |
| | 521 | the screen width. In that case, it seems to be convenient to use the scroll of |
| | 522 | the browser.</span></p> |
| | 523 | |
| | 524 | <p class=MsoNormal><span lang=EN-US>After manipulating the previous items, |
| | 525 | press the “Apply” button to shifting to the desired position of the sequence.</span></p> |
| | 526 | |
| | 527 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 528 | |
| | 529 | <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Using |
| | 530 | shifting button method</span></h3> |
| | 531 | |
| | 532 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 533 | border=0 width=267 height=25 src="manual_e.files/image010.jpg" |
| | 534 | alt="browser_moves.png"></span></p> |
| | 535 | |
| | 536 | <p class=MsoNormal><span lang=EN-US>Moreover, there is another method by using |
| | 537 | the button (like above image). Normally, the input box method is useful only when |
| | 538 | it is important to have the correct position of the sequence. As number |
| | 539 | must be supplied in this method, sometime this process is quit cumbersome. So |
| | 540 | we provide more intuitive methods for your convenience. So the buttons related |
| | 541 | to these methods are as follows,</span></p> |
| | 542 | |
| | 543 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 544 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 545 | </span></span><b><span lang=EN-US>Shifting (</span></b><span lang=EN-US><img |
| | 546 | border=0 width=18 height=13 src="manual_e.files/image011.jpg" alt=rr.png><b>,</b><img |
| | 547 | border=0 width=13 height=13 src="manual_e.files/image012.jpg" alt=r.png><b>,</b><img |
| | 548 | border=0 width=13 height=13 src="manual_e.files/image013.jpg" alt=f.png><b>,</b><img |
| | 549 | border=0 width=18 height=13 src="manual_e.files/image014.jpg" alt=ff.png><b>): |
| | 550 | </b><img border=0 width=18 height=13 src="manual_e.files/image011.jpg" |
| | 551 | alt=rr.png><b>,</b><img border=0 width=13 height=13 |
| | 552 | src="manual_e.files/image012.jpg" alt=r.png><b>,</b><img border=0 width=13 |
| | 553 | height=13 src="manual_e.files/image013.jpg" alt=f.png><b>,</b><img border=0 |
| | 554 | width=18 height=13 src="manual_e.files/image015.jpg" alt=ff.png> are buttons to |
| | 555 | shifting the sequence. The<img border=0 width=18 height=13 |
| | 556 | src="manual_e.files/image011.jpg" alt=rr.png> button scrolls sequence up to one |
| | 557 | screen size where the <img border=0 width=13 height=13 |
| | 558 | src="manual_e.files/image012.jpg" alt=r.png> button scrolls half screen to |
| | 559 | the left. The inverse buttons are for shifting to the right. </span></p> |
| | 560 | |
| | 561 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 562 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 563 | </span></span><b><span lang=EN-US>Scaling (<img border=0 width=13 height=13 |
| | 564 | src="manual_e.files/image016.jpg" alt=zoomout.png>, <img border=0 width=13 |
| | 565 | height=13 src="manual_e.files/image017.jpg" alt=zoomin.png>, <img border=0 |
| | 566 | width=18 height=13 src="manual_e.files/image018.jpg" alt=zoom10x.png>, <img |
| | 567 | border=0 width=18 height=13 src="manual_e.files/image019.jpg" alt=zoom1x.png>, <img |
| | 568 | border=0 width=18 height=13 src="manual_e.files/image020.jpg" alt=zoom01x.png>, |
| | 569 | <img border=0 width=18 height=13 src="manual_e.files/image021.jpg" |
| | 570 | alt=zoom001x.png>, <img border=0 width=18 height=13 |
| | 571 | src="manual_e.files/image022.jpg" alt=zoom0001x.png>): </span></b><span |
| | 572 | lang=EN-US>The <b><img border=0 width=13 height=13 |
| | 573 | src="manual_e.files/image016.jpg" alt=zoomout.png></b> button does scaling |
| | 574 | down and the display will be half of the present size where <b><img border=0 |
| | 575 | width=13 height=13 src="manual_e.files/image017.jpg" alt=zoomin.png></b> button |
| | 576 | does scaling up and the display will be 2 times bigger than present size. The |
| | 577 | fractional form button specifies the scale directly. The scaling unit is |
| | 578 | 1bp/pixel. For example, <b><img border=0 width=18 height=13 |
| | 579 | src="manual_e.files/image019.jpg" alt=zoom1x.png></b> means 1 bp is |
| | 580 | displayed by 1 pixel, whereas <b><img border=0 width=18 height=13 |
| | 581 | src="manual_e.files/image023.jpg" alt=zoom01x.png></b> means 10 bp is |
| | 582 | displayed by 1 pixel. So <b><img border=0 width=18 height=13 |
| | 583 | src="manual_e.files/image018.jpg" alt=zoom10x.png></b> means the scale |
| | 584 | that enlarges the display up to the base level.<span style='color:red'> </span><b><img |
| | 585 | border=0 width=18 height=13 src="manual_e.files/image024.jpg" |
| | 586 | alt=zoom0001x.png></b><span style='color:red'> </span>is a scale ratio |
| | 587 | useful in displaying 1M bps on the screen.<span style='color:red'> </span> At |
| | 588 | the time of scaling up or down the view points of the present display will be |
| | 589 | remained unchanged.<span style='color:red'> </span></span></p> |
| | 590 | |
| | 591 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 592 | |
| | 593 | <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Using |
| | 594 | overview, ruler and zooming track method</span></h3> |
| | 595 | |
| | 596 | <p class=MsoNormal><span lang=EN-US>In addition, there are some methods to |
| | 597 | shifting. These are overview, ruler, zooming trucks. You can shift the |
| | 598 | viewpoint by clicking any position of these tracks. For details, please refer |
| | 599 | to the respective details about the each track.</span></p> |
| | 600 | |
| | 601 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 602 | |
| | 603 | <h2><span lang=EN-US>4.2. Functions of buttons</span></h2> |
| | 604 | |
| | 605 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 606 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 607 | </span></span><b><span lang=EN-US>(rev) </span></b><span lang=EN-US>You |
| | 608 | can display the sequence in reverse mode by UT Genome Browser. Normally a sequence |
| | 609 | is displayed from left to right but you can reverse it with the (rev) button. An |
| | 610 | alternative way to display in reverse way is to input “start” value greater |
| | 611 | than “end” value in the Input Box. The same task can be done easily by clicking |
| | 612 | the (rev) button. As the (rev) button reverses start and end points of the |
| | 613 | present displayed sequence so this can change the display mode from normal to |
| | 614 | reverse or vice versa.<b> </b>If you press the (fasta) button on reverse mode, |
| | 615 | then the complementary strand of displayed strand will be retrieved.</span></p> |
| | 616 | |
| | 617 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 618 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 619 | </span></span><b><span lang=EN-US>(top) </span></b><span lang=EN-US>By |
| | 620 | pressing this button you can return to the main screen. Information about |
| | 621 | present displayed range, track and each track setting etc. will be preserved.</span></p> |
| | 622 | |
| | 623 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 624 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 625 | </span></span><b><span lang=EN-US>(clear) </span></b><span lang=EN-US>By |
| | 626 | pressing this button you can return to the main screen. Information about |
| | 627 | present displayed range, track and each track setting etc. will be initialized. |
| | 628 | </span></p> |
| | 629 | |
| | 630 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 631 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 632 | </span></span><b><span lang=EN-US>(Track) </span></b><span lang=EN-US>Addition, |
| | 633 | deletion, and rearranging can be performed by this button. Details description |
| | 634 | will be given later.</span></p> |
| | 635 | |
| | 636 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 637 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 638 | </span></span><b><span lang=EN-US>(fasta) </span></b><span lang=EN-US>Present |
| | 639 | displaying sequence can be retrieved with this button in fasta format. You will |
| | 640 | be instructed to save as a file name. For example,<b> </b>Medaka-200406-scaffold429 |
| | 641 | (64587-66612). fasta</span></p> |
| | 642 | |
| | 643 | <p class=MsoNormal><span lang=EN-US style='color:red'> </span></p> |
| | 644 | |
| | 645 | <h2><span lang=EN-US>4.3. Addition, Deletion, and Rearrangement of Tracks</span></h2> |
| | 646 | |
| | 647 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 648 | border=0 width=348 height=320 src="manual_e.files/image025.jpg" |
| | 649 | alt="browser_track.png"></span></p> |
| | 650 | |
| | 651 | <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'> </span></b></p> |
| | 652 | |
| | 653 | <p class=MsoNormal><span lang=EN-US>When the (track) button of the main screen |
| | 654 | is pressed, the above track-editing screen will pop up. Here you can do addition, |
| | 655 | deletion and rearrangement of the tracks. This editing screen can be divided |
| | 656 | into three parts - displaying tracks, removed tracks, and adding new track.</span></p> |
| | 657 | |
| | 658 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 659 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 660 | </span></span><b><span lang=EN-US>Displaying track: </span></b><span |
| | 661 | lang=EN-US>Here, tracks’ deletion and rearrangement can be done to the present |
| | 662 | displayed screen. The deleted tracks will be replaced to next removed track. </span></p> |
| | 663 | |
| | 664 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 665 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 666 | </span></span><b><span lang=EN-US>Removed track: </span></b><span lang=EN-US>This |
| | 667 | is the list of all tracks, which are deleted at Displaying Tracks. It is something |
| | 668 | like garbage bin. Undo-processing is possible for the tracks that are displayed |
| | 669 | here.</span></p> |
| | 670 | |
| | 671 | <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span |
| | 672 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 673 | </span></span><b><span lang=EN-US>Add new track: </span></b><span lang=EN-US>New |
| | 674 | tracks, which are not available at present display, can be added by this track. |
| | 675 | By setting the URL of the new tracks, push add button. If the new tracks’ URL |
| | 676 | is read properly, the new tracks will be added after the present displayed |
| | 677 | tracks. </span></p> |
| | 678 | |
| | 679 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 680 | |
| | 681 | <h2><span lang=EN-US>4.4. Setting for Tracks</span></h2> |
| | 682 | |
| | 683 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 684 | border=0 width=358 height=288 src="manual_e.files/image026.jpg"></span></p> |
| | 685 | |
| | 686 | <p class=MsoNormal><span lang=EN-US>On main screen, when the <img border=0 |
| | 687 | width=9 height=9 src="manual_e.files/image027.jpg" alt=cfg.png> button, |
| | 688 | beside the track name, is pressed, the display of that track can be customized |
| | 689 | as above image. The customizing contents of the tracks differ from each other. |
| | 690 | On the other hand, there are some tracks which contents cannot be customized at |
| | 691 | all. For details, please refer to the individual tracks information. |
| | 692 | </span></p> |
| | 693 | |
| | 694 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 695 | |
| | 696 | <h1><span lang=EN-US>5. Pre-defined Tracks</span></h1> |
| | 697 | |
| | 698 | <h2><span lang=EN-US>5.1. Overview Track</span></h2> |
| | 699 | |
| | 700 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 701 | border=0 width=552 height=15 src="manual_e.files/image028.jpg" |
| | 702 | alt="track_overview.png"></span></p> |
| | 703 | |
| | 704 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US |
| | 705 | style='font-size:12.0pt;font-family:"ＭＳ 明朝"'> </span></p> |
| | 706 | |
| | 707 | <p class=MsoNormal><span lang=EN-US>This track shows the range of present |
| | 708 | displayed window in the total genome. In above image, for instance, the |
| | 709 | blue-colored viewpoint shows the range from 125kb to 145kb. Clicking on any |
| | 710 | position of this overview track moves the viewpoint the middle position. For |
| | 711 | example, when you click on around 100k positions, the viewpoint will move to |
| | 712 | 90k-110k. </span></p> |
| | 713 | |
| | 714 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 715 | |
| | 716 | <h2><span lang=EN-US>5.2. Ruler and Zooming Tracks</span></h2> |
| | 717 | |
| | 718 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 719 | border=0 width=566 height=9 src="manual_e.files/image029.jpg"></span></p> |
| | 720 | |
| | 721 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 722 | border=0 width=566 height=9 src="manual_e.files/image030.jpg"></span></p> |
| | 723 | |
| | 724 | <p class=MsoNormal><span lang=EN-US>Both the ruler track and the zooming track |
| | 725 | are displaying same contents with different color. These two show the base |
| | 726 | position number of the present displayed content with respect to the total |
| | 727 | sequence. If you click any position of the ruler track, the viewpoint |
| | 728 | will move to the middle position. For example, if the rightmost end of the |
| | 729 | ruler track is clicked then the same effect will be happed as the <img |
| | 730 | border=0 width=15 height=10 src="manual_e.files/image031.jpg" alt=ff.png> button |
| | 731 | of main screen is pressed. Before using the zoom button on main screen, it is |
| | 732 | better to have the required region on middle position by using the ruler track |
| | 733 | to smoothing future enlarge processing.</span></p> |
| | 734 | |
| | 735 | <p class=MsoNormal style='text-indent:5.25pt'><span lang=EN-US>In addition to |
| | 736 | the effect of the ruler track, if you click any position on the zooming track |
| | 737 | then two times zoom will be happened. For example, it is same to click the |
| | 738 | central button on zoom track as the <img border=0 width=13 height=13 |
| | 739 | src="manual_e.files/image017.jpg" alt=zoomin.png> button on main screen. |
| | 740 | On the other hand, it is also same to clicking the rightmost end of the zooming |
| | 741 | track as click <img border=0 width=18 height=13 |
| | 742 | src="manual_e.files/image014.jpg" alt=ff.png> then click <img border=0 |
| | 743 | width=13 height=13 src="manual_e.files/image017.jpg" alt=zoomin.png> on |
| | 744 | main screen. This track is useful to zoom out our interested region on the |
| | 745 | sequence..</span></p> |
| | 746 | |
| | 747 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 748 | |
| | 749 | <h2><span lang=EN-US>5.3. Base Color Track</span></h2> |
| | 750 | |
| | 751 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 752 | border=0 width=566 height=9 src="manual_e.files/image032.jpg"><img border=0 |
| | 753 | width=566 height=9 src="manual_e.files/image033.jpg"></span></p> |
| | 754 | |
| | 755 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US> </span></p> |
| | 756 | |
| | 757 | <p class=MsoNormal><span lang=EN-US>Base color track changes the sequence to |
| | 758 | color mode. All four ATGC bases are displayed by converting to the individual color. |
| | 759 | It is natural to display each base pair by one pixel. By zooming in, you can |
| | 760 | see any specific region of the sequence in alphabet symbol (above bottom |
| | 761 | image). </span></p> |
| | 762 | |
| | 763 | <p class=MsoNormal style='text-indent:5.25pt'><span lang=EN-US>It is also possible |
| | 764 | to customize the corresponding base pair color also. For example, if GC base |
| | 765 | pair are only colored then we can use it as a simple GC content track. To get |
| | 766 | the sequence itself, it is better to save from fasta track.</span></p> |
| | 767 | |
| | 768 | <p class=MsoNormal><span lang=EN-US style='color:red'> </span></p> |
| | 769 | |
| | 770 | <h2><span lang=EN-US>5.4. Gap Track</span></h2> |
| | 771 | |
| | 772 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 773 | border=0 width=566 height=7 src="manual_e.files/image034.jpg"></span></p> |
| | 774 | |
| | 775 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US> </span></p> |
| | 776 | |
| | 777 | <p class=MsoNormal><span lang=EN-US>Gap Track is a track that displays gaps in |
| | 778 | a scaffold. By clicking any place except the gap, we can get the whole contig |
| | 779 | sequence in FASTA format. It is different from the (fasta) button in the main |
| | 780 | window, because it does not retrieve the displayed sequence only, but saves the |
| | 781 | whole contig sequence.</span></p> |
| | 782 | |
| | 783 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 784 | |
| | 785 | <h2><span lang=EN-US>5.5. GC Content Track</span></h2> |
| | 786 | |
| | 787 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 788 | border=0 width=566 height=28 src="manual_e.files/image035.jpg"></span></p> |
| | 789 | |
| | 790 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 791 | |
| | 792 | <p class=MsoNormal><span lang=EN-US>This track displays the ratio of GC |
| | 793 | contents for 5 pixels. If the pixel number of a base pair is more than 5, the |
| | 794 | coloring will be done to tell whether it is GC or AT. </span></p> |
| | 795 | |
| | 796 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 797 | |
| | 798 | <h2><span lang=EN-US>5.6. Mapped Gene Track</span></h2> |
| | 799 | |
| | 800 | <p class=MsoNormal align=center style='margin-right:-60.8pt;text-align:center'><span |
| | 801 | lang=EN-US><img border=0 width=566 height=58 src="manual_e.files/image036.jpg"></span></p> |
| | 802 | |
| | 803 | <p class=MsoNormal style='margin-right:-60.8pt'><span lang=EN-US> </span></p> |
| | 804 | |
| | 805 | <p class=MsoNormal><span lang=EN-US>This track displays the mapping result of |
| | 806 | Fugu, Zebra fish and Medaka’s Est to the Medaka genome, done by ALPS (<a href="http://alps.gi.k.u-tokyo.ac.jp">http://alps.gi.k.u-tokyo.ac.jp</a>). The |
| | 807 | mapping region for the gene is displayed by line and the exons are shown in rectangular |
| | 808 | box. The arrow sign shows the plus or minus strand of the genome. The above |
| | 809 | image displays Medaka’s ESTs in black color, while the green color indicates |
| | 810 | cDNAs of Fugu. The current data sources of mapped genes are Medaka Unigene |
| | 811 | Build#10, Zebra fish Unigene Build#71, and Fugu ensemble pufferfish v21.2.c1( |
| | 812 | 10<sup>th</sup> May, 2004). We will revise the alignment periodically in |
| | 813 | response to the update of the data sources.</span></p> |
| | 814 | |
| | 815 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 816 | |
| | 817 | <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Display |
| | 818 | setting</span></h3> |
| | 819 | |
| | 820 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 821 | border=0 width=358 height=288 src="manual_e.files/image037.jpg"></span></p> |
| | 822 | |
| | 823 | <p class=MsoNormal><span lang=EN-US>If the <img border=0 width=9 height=9 |
| | 824 | src="manual_e.files/image027.jpg" alt=cfg.png> button on the left side of |
| | 825 | Mapped Gene Track is pressed, the display setting windows will pop up. There |
| | 826 | are three parts of this setting; namely, changing the total display style, |
| | 827 | alternating the mapping results if a gene will be displayed or not, and modifying |
| | 828 | the color of a gene. The setting, whether to show or not, will display all |
| | 829 | which fulfill the conditions. The color setting can be done by “use this color” |
| | 830 | button beside the track. </span></p> |
| | 831 | |
| | 832 | <p class=MsoNormal><b><span lang=EN-US>Style select setting</span></b></p> |
| | 833 | |
| | 834 | <p class=MsoNormal><span lang=EN-US>Predicted genes’ display setting can be |
| | 835 | changed here. There are four kinds of display style. These styles are full, |
| | 836 | pack, small and dense. </span></p> |
| | 837 | |
| | 838 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 839 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 840 | </span></span><b><span lang=EN-US>Full:</span></b><span lang=EN-US> In full |
| | 841 | style, each gene’s position is displayed on one line. On left side the Genebank |
| | 842 | accession number or Ensemble Gene ID is written. <br> |
| | 843 | <img border=0 width=489 height=156 src="manual_e.files/image038.jpg"></span></p> |
| | 844 | |
| | 845 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 846 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 847 | </span></span><b><span lang=EN-US>Pack:</span></b><span lang=EN-US> By showing |
| | 848 | individual alignments together with the names (Genebank Acc or Ensemble Gene |
| | 849 | ID) of genes on left side in multiple on one line, the pack style is more |
| | 850 | compact than full style.<br> |
| | 851 | <img border=0 width=488 height=50 src="manual_e.files/image039.jpg"></span></p> |
| | 852 | |
| | 853 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 854 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 855 | </span></span><b><span lang=EN-US>Small:</span></b><span lang=EN-US> In small |
| | 856 | style, the up and down spaces for one gene are reduced to the minimum. Unlike |
| | 857 | the full style and the pack style, this does not display the names of the |
| | 858 | genes.<br> |
| | 859 | |
| | 860 | <img border=0 width=488 height=17 src="manual_e.files/image040.jpg"></span></p> |
| | 861 | |
| | 862 | <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span |
| | 863 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 864 | </span></span><b><span lang=EN-US>Dense:</span></b><span lang=EN-US> In this |
| | 865 | style, only the positions of aligned exons are displayed on one line.<br> |
| | 866 | <img border=0 width=484 height=8 src="manual_e.files/image041.jpg"></span></p> |
| | 867 | |
| | 868 | <p class=MsoNormal><span lang=EN-US>At present except the full style, if the |
| | 869 | numbers of the mapped genes are more than 200 in a range of more than 50kbp, the |
| | 870 | graphical view of the genes will be displayed.</span></p> |
| | 871 | |
| | 872 | <p class=MsoNormal><b><span lang=EN-US>FormSpecies disp setting</span></b></p> |
| | 873 | |
| | 874 | <p class=MsoNormal><span lang=EN-US>Here we can set which species among Medaka, |
| | 875 | Zebra fish, Fugu’s mapping results are displayed or not. On default, all |
| | 876 | species results will be displayed. Only the species, which are checked on the |
| | 877 | Checkbook, will be displayed. </span></p> |
| | 878 | |
| | 879 | <p class=MsoNormal><b><span lang=EN-US>FromSpecies color setting </span></b></p> |
| | 880 | |
| | 881 | <p class=MsoNormal><span lang=EN-US>The color distinguishing for Medaka, Zebra |
| | 882 | fish, Fugu’s can be done here.</span></p> |
| | 883 | |
| | 884 | <p class=MsoNormal><b><span lang=EN-US>MatchRatio gradation setting</span></b></p> |
| | 885 | |
| | 886 | <p class=MsoNormal><span lang=EN-US>Gene’s color can be changed with respect to |
| | 887 | its match ratio. Provided colors for the match ratios 0.7 and 1.0 respectively, |
| | 888 | the system automatically gradates the coloring of the alignments between the |
| | 889 | lower and upper match ratios. </span></p> |
| | 890 | |
| | 891 | <p class=MsoNormal><b><span lang=EN-US>MatchRatio ulbound setting</span></b></p> |
| | 892 | |
| | 893 | <p class=MsoNormal><span lang=EN-US>You can specify the range of the mapping |
| | 894 | ratio by inputting the lower and upper bounds into the corresponding boxes. |
| | 895 | Alignments of match ratios within the range are only displayed.</span></p> |
| | 896 | |
| | 897 | <p class=MsoNormal><b><span lang=EN-US>CoverRatio gradation setting</span></b></p> |
| | 898 | |
| | 899 | <p class=MsoNormal><span lang=EN-US>Gene’s color can also be changed with |
| | 900 | respect to its cover ratio. Provided colors for the cover ratios 0.4 and 1.0 |
| | 901 | respectively, the system automatically gradates the coloring of the alignments |
| | 902 | between the lower and upper cover ratios. </span></p> |
| | 903 | |
| | 904 | <p class=MsoNormal><b><span lang=EN-US>CoverRatio ulbound setting</span></b></p> |
| | 905 | |
| | 906 | <p class=MsoNormal><span lang=EN-US>You can specify the range of the cover |
| | 907 | ratio by inputting the lower and upper bounds into the corresponding boxes. |
| | 908 | Alignments of cover ratios within the range are only displayed.</span></p> |
| | 909 | |
| | 910 | <p class=MsoNormal><b><span lang=EN-US>Stage disp setting</span></b></p> |
| | 911 | |
| | 912 | <p class=MsoNormal><span lang=EN-US>Here, you can fix which development stage’s |
| | 913 | expression EST should be displayed. </span></p> |
| | 914 | |
| | 915 | <p class=MsoNormal><b><span lang=EN-US>Stage color setting</span></b></p> |
| | 916 | |
| | 917 | <p class=MsoNormal><span lang=EN-US>Color distinguishing can be done with |
| | 918 | respect to development stage.</span></p> |
| | 919 | |
| | 920 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 921 | |
| | 922 | <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Linkage |
| | 923 | for each gene </span></h3> |
| | 924 | |
| | 925 | <p class=MsoNormal><span lang=EN-US>In full, pack and small style, each gene |
| | 926 | can be clicked on. By clicking each gene, you can see the details of this gene.</span></p> |
| | 927 | |
| | 928 | <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'> </span></b></p> |
| | 929 | |
| | 930 | <h2><span lang=EN-US>5.7. Genscan Track</span></h2> |
| | 931 | |
| | 932 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 933 | border=0 width=567 height=39 src="manual_e.files/image042.jpg"></span></p> |
| | 934 | |
| | 935 | <p class=MsoNormal><span lang=EN-US>This track displays the predicted genes by |
| | 936 | Genscan. The predicted genes are viewed on lines, where the exons parts are on rectangular |
| | 937 | shape. Arrow sign presents the strand of the genes. The above image shows the |
| | 938 | predicted genes in pack style. </span></p> |
| | 939 | |
| | 940 | <p class=MsoNormal><b><span lang=EN-US>Display settings</span></b></p> |
| | 941 | |
| | 942 | <p class=MsoNormal><span lang=EN-US>If the <img border=0 width=9 height=9 |
| | 943 | src="manual_e.files/image027.jpg" alt=cfg.png> mark button on the left |
| | 944 | side of Genscan Track is clicked, the display setting will pop up. Here are the |
| | 945 | details of this setting. </span></p> |
| | 946 | |
| | 947 | <p class=MsoNormal><b><span lang=EN-US>Style selects setting</span></b></p> |
| | 948 | |
| | 949 | <p class=MsoNormal><span lang=EN-US>Predicted genes’ display setting can be |
| | 950 | changed here. There are four kinds of display style. These styles are full, |
| | 951 | pack, small and dense, and they are similar to those styles in Mapped Gene |
| | 952 | Track.</span></p> |
| | 953 | |
| | 954 | <p class=MsoNormal><b><span lang=EN-US>Linkage of each gene</span></b></p> |
| | 955 | |
| | 956 | <p class=MsoNormal><span lang=EN-US>In full, pack and small style each gene can |
| | 957 | be clicked on. After clicking each gene, the details of prediction by Genscan |
| | 958 | will be appeared.</span></p> |
| | 959 | |
| | 960 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 961 | |
| | 962 | <h2><span lang=EN-US>5.8. Comparative Genomics Track</span></h2> |
| | 963 | |
| | 964 | <p class=MsoNormal><b><span lang=EN-US style='font-size:12.0pt'>Fugu Scaffold |
| | 965 | track</span></b></p> |
| | 966 | |
| | 967 | <p class=MsoNormal><b><span lang=EN-US>Description</span></b></p> |
| | 968 | |
| | 969 | <p class=MsoNormal><span lang=EN-US>This track shows Fugu/Medaka homologous |
| | 970 | scaffolds detected by ALPS alignment program. Fugu scaffolds are denoted by |
| | 971 | boxes connected by arrows. The boxes represent regions of high homology (match |
| | 972 | ratio > 60%) aligned by ALPS. The arrows represent low homology regions or |
| | 973 | gaps in Fugu scaffold. The direction of arrows indicates the orientation |
| | 974 | of Fugu/Medaka alignments. Clicking on a Fugu scaffold will open a new window |
| | 975 | to display its dotplot with Fugu scaffold sequence provided in the same page. |
| | 976 | The Fugu sequence (Fugu v.2.0) was downloaded from JGI.</span></p> |
| | 977 | |
| | 978 | <p class=MsoNormal><b><span lang=EN-US>Method</span></b></p> |
| | 979 | |
| | 980 | <p class=MsoNormal><span lang=EN-US>Fugu scaffold sequences are split into |
| | 981 | non-overlapping 300mer sequences and these 300mer sequences are mapped to |
| | 982 | Medaka scaffolds with ALPS. ALPS alignments with match ratio less than 60% are |
| | 983 | discarded and remaining alignments are chained by longest monotone subsequence |
| | 984 | algorithm. Chains consist of more than 10 alignments are displayed in the |
| | 985 | track. Note that inversions or microrearrangements are not shown. Only the longest |
| | 986 | monotone subsequence is displayed for each Fugu scaffold.</span></p> |
| | 987 | |
| | 988 | <p class=MsoNormal><b><span lang=EN-US>Linkage of each scaffold </span></b></p> |
| | 989 | |
| | 990 | <p class=MsoNormal><span lang=EN-US>In full, pack and small style each gene can |
| | 991 | be clicked on. After clicking each scaffold, the detailed alignments will be |
| | 992 | appeared as like dot plot. Dotplot shows homologous regions of Fugu/Medaka |
| | 993 | scaffolds as diagonal runs of dots. Each dot, plotted based on sequence |
| | 994 | similarity score, indicates that significantly many seed matches are found |
| | 995 | between corresponding regions. The sequence similarity score is defined in such |
| | 996 | a way that tandem repeats are not assigned high scores while unique sequences |
| | 997 | are assigned high scores.</span></p> |
| | 998 | |
| | 999 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img |
| | 1000 | border=0 width=567 height=201 src="manual_e.files/image043.jpg"></span></p> |
| | 1001 | |
| | 1002 | <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US> </span></p> |
| | 1003 | |
| | 1004 | <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US> </span></b></p> |
| | 1005 | |
| | 1006 | <span lang=EN-US style='font-size:10.5pt;font-family:Century'><br clear=all |
| | 1007 | style='page-break-before:always'> |
| | 1008 | |
| | 1009 | </span> |
| | 1010 | |
| | 1011 | <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>Ramen Assembler |
| | 1012 | / UT Genome Browser Team Members</span></b></p> |
| | 1013 | |
| | 1014 | <p class=MsoNormal><span lang=EN-US><br> |
| | 1015 | Ramen Genome Assembler Development Team</span></p> |
| | 1016 | |
| | 1017 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1018 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1019 | </span></span><span lang=EN-US>Development of “Ramen” genome assembler and |
| | 1020 | assembly of medaka genome:<br> |
| | 1021 | Masahiro Kasahara and Shin Sasaki</span></p> |
| | 1022 | |
| | 1023 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1024 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1025 | </span></span><span lang=EN-US>Development of “Ramen Viewer” for genome |
| | 1026 | assembly: <br> |
| | 1027 | |
| | 1028 | Yukinobu Nagayasu</span></p> |
| | 1029 | |
| | 1030 | <p class=MsoNormal><span lang=EN-US><br> |
| | 1031 | UT Genome Browser Development Team</span></p> |
| | 1032 | |
| | 1033 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1034 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1035 | </span></span><span lang=EN-US>Design and development of UT Genome Browser, |
| | 1036 | keyword search function, libraries for describing tracks: <br> |
| | 1037 | Yukinobu Nagayasu and Koichiro Doi</span></p> |
| | 1038 | |
| | 1039 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1040 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1041 | </span></span><span lang=EN-US>Online mapping function for query sequences:<br> |
| | 1042 | Tomoyuki Yamada</span></p> |
| | 1043 | |
| | 1044 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1045 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1046 | </span></span><span lang=EN-US>Comparative Genomics Track:<br> |
| | 1047 | Yoichiro Nakatani and Wei Qu</span></p> |
| | 1048 | |
| | 1049 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1050 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1051 | </span></span><span lang=EN-US>Gene Prediction:<br> |
| | 1052 | Ahsan Budrul</span></p> |
| | 1053 | |
| | 1054 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1055 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1056 | </span></span><span lang=EN-US>Mapped Gene Track:<br> |
| | 1057 | Yasuhiro Kasai</span></p> |
| | 1058 | |
| | 1059 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1060 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1061 | </span></span><span lang=EN-US>Database access accelerators:<br> |
| | 1062 | Takehiro Furudate and Atsushi Mori</span></p> |
| | 1063 | |
| | 1064 | <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span |
| | 1065 | lang=EN-US style='font-family:Wingdings'>ü<span style='font:7.0pt "Times New Roman"'> |
| | 1066 | </span></span><span lang=EN-US>Overall management:<br> |
| | 1067 | Koichiro Doi and Shinichi Morishita</span></p> |
| | 1068 | |
| | 1069 | <p class=MsoNormal><span lang=EN-US> </span></p> |
| | 1070 | |
| | 1071 | <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>Acknowledgements</span></b></p> |
| | 1072 | |
| | 1073 | <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'> </span></b></p> |
| | 1074 | |
| | 1075 | <p class=MsoNormal><span lang=EN-US>This work has been supported by |
| | 1076 | Grant-in-Aid for Scientific Research on Priority Areas (Grant#12209003) to |
| | 1077 | Shinichi Morishita. </span></p> |
| | 1078 | |
| | 1079 | <p class=MsoNormal><span lang=EN-US>Ramen Assembler Development Team members |
| | 1080 | are indebted to Yuji Kohara and Tadasu Shin-i for their technical discussions |
| | 1081 | on the whole genome shotgun assembly.</span></p> |
| | 1082 | |
| | 1083 | <p class=MsoNormal><span lang=EN-US>Members in the UT Genome Browser |
| | 1084 | Development Team are grateful to Kiyoshi Naruse, Daisuke Kobayashi, and |
| | 1085 | Takanori Narita for their valuable input to improve the functions of the |
| | 1086 | browser in a variety of ways.</span></p> |
| | 1087 | |
| | 1088 | </div> |
| | 1089 | }}} |
