Changes between Version 3 and Version 4 of UTGBManual


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Timestamp:
08/15/07 15:25:44 (18 years ago)
Author:
leo
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  • UTGBManual

    v3 v4  
    11= UTGB Manual =
    2 {{{
    3 #!html
    4 <style>
    5 
    6 
    7 <div class=Section1 style='layout-grid:18.0pt'>
    8 
    9 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    10 24.0pt'>&nbsp;</span></h1>
    11 
    12 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    13 24.0pt'>&nbsp;</span></h1>
    14 
    15 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    16 36.0pt'>UT Genome Browser</span></h1>
    17 
    18 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    19 36.0pt'>&nbsp;</span></h1>
    20 
    21 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    22 36.0pt'>User’s Manual</span></h1>
    23 
    24 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    25 36.0pt'>Version 1.0</span></h1>
    26 
    27 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    28 24.0pt'>&nbsp;</span></h1>
    29 
    30 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    31 
    32 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    33 
    34 <p class=MsoNormal align=center style='text-align:center'><b><span
    35  lang=EN-US style='font-size:24.0pt'>August 17, 2004</span></b></p>
    36 
    37 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    38 24.0pt'>&nbsp;</span></h1>
    39 
    40 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    41 
    42 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    43 
    44 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    45 22.0pt'>UT Genome Browser Development Team</span></h1>
    46 
    47 <h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
    48 22.0pt'>&nbsp;</span></h1>
    49 
    50 <b><span lang=EN-US style='font-size:18.0pt;font-family:Century'><br clear=all
    51 style='page-break-before:always'>
    52 </span></b>
    53 
    54 <h1><span lang=EN-US>Table of Contents</span></h1>
    55 
    56 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    57 
    58 <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
    59 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>1<span
    60 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    61 </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Welcome</span></b></p>
    62 
    63 <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
    64 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2<span
    65 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    66 </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Keyword
    67 Search</span></b></p>
    68 
    69 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    70 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2.1<span
    71 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    72 lang=EN-US style='font-size:14.0pt;line-height:150%'>Gene List</span></b></p>
    73 
    74 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    75 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2.2<span
    76 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    77 lang=EN-US style='font-size:14.0pt;line-height:150%'>Mapping Position List</span></b></p>
    78 
    79 <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
    80 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>3<span
    81 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    82 </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Online
    83 Sequence Alignment</span></b></p>
    84 
    85 <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
    86 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4<span
    87 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    88 
    89 </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Main
    90 Window</span></b></p>
    91 
    92 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    93 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.1<span
    94 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    95 lang=EN-US style='font-size:14.0pt;line-height:150%'>Scrolling and Zooming the
    96 Main Window</span></b></p>
    97 
    98 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    99 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.2<span
    100 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    101 lang=EN-US style='font-size:14.0pt;line-height:150%'>Functions of Buttons</span></b></p>
    102 
    103 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    104 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.3<span
    105 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    106 lang=EN-US style='font-size:14.0pt;line-height:150%'>Addition, Deletion, and
    107 Rearrangement of Tracks</span></b></p>
    108 
    109 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    110 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.4<span
    111 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    112 lang=EN-US style='font-size:14.0pt;line-height:150%'>Setting for Tracks</span></b></p>
    113 
    114 <p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
    115 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5<span
    116 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    117 </span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Pre-defined
    118 Tracks</span></b></p>
    119 
    120 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    121 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.1<span
    122 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    123 lang=EN-US style='font-size:14.0pt;line-height:150%'>Overview Tracks</span></b></p>
    124 
    125 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    126 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.2<span
    127 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    128 lang=EN-US style='font-size:14.0pt;line-height:150%'>Ruler and Zooming Tracks</span></b></p>
    129 
    130 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    131 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.3<span
    132 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    133 lang=EN-US style='font-size:14.0pt;line-height:150%'>Base Color Track</span></b></p>
    134 
    135 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    136 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.4<span
    137 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    138 lang=EN-US style='font-size:14.0pt;line-height:150%'>Gap Track</span></b></p>
    139 
    140 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    141 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.5<span
    142 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    143 lang=EN-US style='font-size:14.0pt;line-height:150%'>GC Content Track</span></b></p>
    144 
    145 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    146 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.6<span
    147 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    148 lang=EN-US style='font-size:14.0pt;line-height:150%'>Mapped Gene Track</span></b></p>
    149 
    150 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    151 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.7<span
    152 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    153 lang=EN-US style='font-size:14.0pt;line-height:150%'>Genscan Track</span></b></p>
    154 
    155 <p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
    156 150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.8<span
    157 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
    158 lang=EN-US style='font-size:14.0pt;line-height:150%'>Comparative Genomics Track</span></b></p>
    159 
    160 <p class=MsoNormal style='line-height:150%'><b><span lang=EN-US
    161 style='font-size:14.0pt;line-height:150%'>Ramen Assembler / UT Genome Browser
    162 Team Members</span></b></p>
    163 
    164 <p class=MsoNormal style='line-height:150%'><b><span lang=EN-US
    165 style='font-size:14.0pt;line-height:150%'>Acknowledgements</span></b></p>
    166 
    167 <span lang=EN-US style='font-size:10.5pt;line-height:150%;font-family:Century'><br
    168 clear=all style='page-break-before:always'>
    169 </span>
    170 
    171 <p class=MsoNormal style='line-height:150%'><span class=a><span lang=EN-US
    172 style='font-size:18.0pt;line-height:150%'>1. Welcome</span></span></p>
    173 
    174 <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
    175 of a target species (at present Medaka only) from several aspects. For example,
    176 the following tasks can be performed with different combinations. </span></p>
    177 
    178 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    179 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    180 </span></span><span lang=EN-US>You can search gene, by gene name, clone name,
    181 cluster name and display its surroundings gene groups.</span></p>
    182 
    183 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    184 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    185 </span></span><span lang=EN-US>You can map a genomic sequence to any genome and
    186 observe its surroundings.</span></p>
    187 
    188 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    189 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    190 </span></span><span lang=EN-US>You can save the sequence itself on your system
    191 from here.</span></p>
    192 
    193 <p class=MsoNormal><span lang=EN-US>Questions, suggestions or comments are
    194 welcome to <a href="mailto:webmaster@utgenome.org">webmaster@utgenome.org</a>.</span></p>
    195 
    196 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    197 
    198 <h1><span lang=EN-US>2. Keyword Search </span></h1>
    199 
    200 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    201 border=0 width=254 height=262 src="manual_e.files/image001.jpg"
    202 alt="keyword_top.png"></span></p>
    203 
    204 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    205 
    206 <p class=MsoNormal><span lang=EN-US>The top window displays the keyword search
    207 engine, as above picture illustrates. Inputting any keyword at the query box, we
    208 can see the detail information about the query. More about keyword search can
    209 be found in the help, written on the same window. In addition, if the keyword
    210 is a part of targets, then all the targets will be displayed. For example, the
    211 keyword “BCD” will match to “ABCD”, “BCDE”, “BCD” and “BCDF” etc. (this is
    212 worked out with using a suffix array.)</span></p>
    213 
    214 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    215 
    216 <h2><span lang=EN-US>2.1. Gene List</span></h2>
    217 
    218 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    219 border=0 width=288 height=235 src="manual_e.files/image002.jpg"
    220 alt="keyword_genes.png"></span></p>
    221 
    222 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    223 
    224 <p class=MsoNormal><span lang=EN-US>When there are many genes for one keyword
    225 search, all genes will be displayed on a list. Pressing the (*) button on the
    226 left side, you can go to the mapped region for the gene. This list appears when
    227 multiple candidate entries are found, typically when class names or part of a
    228 gene number are input as a keyword. If a Genebank accession number is given,
    229 the number must be unique, and hence this list does not appear.&nbsp; </span></p>
    230 
    231 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    232 
    233 <h2><span lang=EN-US>2.2. Mapping Position List</span></h2>
    234 
    235 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    236 border=0 width=384 height=230 src="manual_e.files/image003.jpg"
    237 alt="keyword_locs.png"></span></p>
    238 
    239 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    240 
    241 <p class=MsoNormal><span lang=EN-US>If the query gene has mapped to several
    242 regions on the genomic sequence, the list of all positions will be shown. Pressing
    243 the (*) button on the left side displays the mapped region of the gene. If
    244 there is only one mapped region of the gene, the list is skipped to display.</span></p>
    245 
    246 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    247 
    248 <h1><span lang=EN-US>3. Sequence Alignment </span></h1>
    249 
    250 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    251 border=0 width=408 height=195 src="manual_e.files/image004.jpg"
    252 alt=online01.PNG></span></p>
    253 
    254 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    255 
    256 <p class=MsoNormal><span lang=EN-US>Sequence mapping is possible by inputting a
    257 sequence in the online mapping frame (above image) at the bottom of the main
    258 window. After selecting the species and its revision, press the search button
    259 on the bottom. The request is sent to the alignment server ALPS to align the
    260 given sequence to the selected genome. Afterwards, the list of alignment
    261 results is returned if the system finds some alignments.</span></p>
    262 
    263 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    264 border=0 width=353 height=431 src="manual_e.files/image005.jpg"></span></p>
    265 
    266 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    267 
    268 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    269 border=0 width=400 height=81 src="manual_e.files/image006.jpg"
    270 alt=online02.PNG></span></p>
    271 
    272 <p class=MsoNormal><span lang=EN-US>From the list, you can select one alignment
    273 by clicking the result button as illustrated above. Then, the aligned result
    274 will appear on the browser. The ALPS mapping track in following snapshot
    275 displays the added mapping status.</span></p>
    276 
    277 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    278 
    279 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    280 border=0 width=566 height=149 src="manual_e.files/image007.jpg"
    281 alt=online03.PNG></span></p>
    282 
    283 <h1><span lang=EN-US>4. Main Window</span></h1>
    284 
    285 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    286 border=0 width=509 height=324 src="manual_e.files/image008.jpg"
    287 alt="browser_main.png"></span></p>
    288 
    289 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    290 
    291 <p class=MsoNormal><span lang=EN-US>The above picture shows the main screen for
    292 UT Genome Browser. It is possible to see the targeted region of genomic
    293 sequence by many tracks. This browser provides the following functions to
    294 manipulate tracks on this image screen.</span></p>
    295 
    296 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    297 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    298 </span></span><span lang=EN-US>Shifting, zooming in and out, and reversing of
    299 the target region. It facilitates zooming in the sequence until bases can be
    300 seen, while providing a panoramic, structural view for the sequence.</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'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    304 </span></span><span lang=EN-US>Adding, deleting and reordering the tracks.</span></p>
    305 
    306 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    307 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    308 </span></span><span lang=EN-US>Customizing of each track’s display.</span></p>
    309 
    310 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    311 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    312 </span></span><span lang=EN-US>Retrieving the present displayed sequence in Fasta
    313 format.</span></p>
    314 
    315 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    316 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    317 </span></span><span lang=EN-US>Continuing keyword search.</span></p>
    318 
    319 <p class=MsoNormal><span lang=EN-US>In what follows, we describe the detail
    320 about each function.</span></p>
    321 
    322 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    323 
    324 <h2><span lang=EN-US>4.1&nbsp;&nbsp; Scrolling and zooming the main window </span></h2>
    325 
    326 <p class=MsoNormal><span lang=EN-US>On main window, it is possible to shift and
    327 to zoom in/out the present observing sequence. These tasks can be carried out
    328 by:</span></p>
    329 
    330 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    331 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    332 </span></span><span lang=EN-US>Inputting value in the input box method.</span></p>
    333 
    334 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    335 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    336 </span></span><span lang=EN-US>Using shifting button method.</span></p>
    337 
    338 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    339 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    340 </span></span><span lang=EN-US>Using overview, ruler and zooming track method.</span></p>
    341 
    342 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    343 
    344 <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Inputting
    345 value in the input box method</span></h3>
    346 
    347 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    348 border=0 width=552 height=31 src="manual_e.files/image009.jpg"
    349 alt="browser_params.png"></span></p>
    350 
    351 <p class=MsoNormal><span lang=EN-US>You can input values into the input boxes
    352 (like above image) inside the main window. The details about this method are as
    353 follows,</span></p>
    354 
    355 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    356 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    357 </span></span><b><span lang=EN-US>Species: </span></b><span lang=EN-US>Select
    358 the species to display. The selectable revisions would be changed with respect
    359 to the species. At present, only Medaka is possible to be selected.</span></p>
    360 
    361 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    362 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    363 </span></span><b><span lang=EN-US>Revision</span></b><span lang=EN-US>: Select
    364 the revision of the target specie’s genome. For Medaka, the revision name
    365 format is yyyymm. The selecting topics will change with respect to the selected
    366 revision.</span></p>
    367 
    368 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    369 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    370 </span></span><b><span lang=EN-US>Target: </span></b><span lang=EN-US>Select
    371 the target region to be displayed, from the selected species and selected
    372 revision. In the case of 200406 revision of Medaka, only scaffold name (e.g.
    373 scaffold123) can be selected but not the chromosome name (e.g. chr10). Chromosome
    374 numbers will be available in our later revision. </span></p>
    375 
    376 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    377 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    378 </span></span><b><span lang=EN-US>Start: </span></b><span lang=EN-US>Select the
    379 start position from your targeted sequence to display. The number should be 1-origin
    380 (i.e. the starting point will be 1).</span></p>
    381 
    382 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    383 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    384 
    385 </span></span><b><span lang=EN-US>End: </span></b><span lang=EN-US>Select the
    386 end point from your targeted sequence to display. The number should be 1-origin.
    387 If the ending point is greater than the starting point then the display will be
    388 normal. Otherwise, the display will be reverse. In both cases, the ending base
    389 will be included in the displaying sequence.</span></p>
    390 
    391 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    392 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    393 </span></span><b><span lang=EN-US>Width: </span></b><span lang=EN-US>Input the
    394 width in terms of pixels for output track display. Input the value that is
    395 suitable for your vision. Normally, it is assumed that width is equal to the
    396 screen width. It is also possible to input the width as 10 times bigger than
    397 the screen width. In that case, it seems to be convenient to use the scroll of
    398 the browser.</span></p>
    399 
    400 <p class=MsoNormal><span lang=EN-US>After manipulating the previous items,
    401 press the “Apply” button to shifting to the desired position of the sequence.</span></p>
    402 
    403 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    404 
    405 <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Using
    406 shifting button method</span></h3>
    407 
    408 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    409 border=0 width=267 height=25 src="manual_e.files/image010.jpg"
    410 alt="browser_moves.png"></span></p>
    411 
    412 <p class=MsoNormal><span lang=EN-US>Moreover, there is another method by using
    413 the button (like above image). Normally, the input box method is useful only when
    414 it is important to have the correct position of the sequence.&nbsp; As number
    415 must be supplied in this method, sometime this process is quit cumbersome. So
    416 we provide more intuitive methods for your convenience. So the buttons related
    417 to these methods are as follows,</span></p>
    418 
    419 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    420 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    421 </span></span><b><span lang=EN-US>Shifting (</span></b><span lang=EN-US><img
    422 border=0 width=18 height=13 src="manual_e.files/image011.jpg" alt=rr.png><b>,</b><img
    423 border=0 width=13 height=13 src="manual_e.files/image012.jpg" alt=r.png><b>,</b><img
    424 border=0 width=13 height=13 src="manual_e.files/image013.jpg" alt=f.png><b>,</b><img
    425 border=0 width=18 height=13 src="manual_e.files/image014.jpg" alt=ff.png><b>):&nbsp;
    426 </b><img border=0 width=18 height=13 src="manual_e.files/image011.jpg"
    427 alt=rr.png><b>,</b><img border=0 width=13 height=13
    428 src="manual_e.files/image012.jpg" alt=r.png><b>,</b><img border=0 width=13
    429 height=13 src="manual_e.files/image013.jpg" alt=f.png><b>,</b><img border=0
    430 width=18 height=13 src="manual_e.files/image015.jpg" alt=ff.png> are buttons to
    431 shifting the sequence. The<img border=0 width=18 height=13
    432 src="manual_e.files/image011.jpg" alt=rr.png> button scrolls sequence up to one
    433 screen size where the <img border=0 width=13 height=13
    434 src="manual_e.files/image012.jpg" alt=r.png>&nbsp;button scrolls half screen to
    435 the left. The inverse buttons are for shifting to the right.&nbsp;&nbsp; </span></p>
    436 
    437 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    438 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    439 </span></span><b><span lang=EN-US>Scaling (<img border=0 width=13 height=13
    440 src="manual_e.files/image016.jpg" alt=zoomout.png>, <img border=0 width=13
    441 height=13 src="manual_e.files/image017.jpg" alt=zoomin.png>, <img border=0
    442 width=18 height=13 src="manual_e.files/image018.jpg" alt=zoom10x.png>, <img
    443 border=0 width=18 height=13 src="manual_e.files/image019.jpg" alt=zoom1x.png>, <img
    444 border=0 width=18 height=13 src="manual_e.files/image020.jpg" alt=zoom01x.png>,
    445 <img border=0 width=18 height=13 src="manual_e.files/image021.jpg"
    446 alt=zoom001x.png>, <img border=0 width=18 height=13
    447 src="manual_e.files/image022.jpg" alt=zoom0001x.png>):&nbsp; </span></b><span
    448 lang=EN-US>The <b><img border=0 width=13 height=13
    449 src="manual_e.files/image016.jpg" alt=zoomout.png></b>&nbsp;button does scaling
    450 down and the display will be half of the present size where <b><img border=0
    451 width=13 height=13 src="manual_e.files/image017.jpg" alt=zoomin.png></b>&nbsp;button
    452 does scaling up and the display will be 2 times bigger than present size. The
    453 fractional form button specifies the scale directly. The scaling unit is
    454 1bp/pixel. For example, <b><img border=0 width=18 height=13
    455 src="manual_e.files/image019.jpg" alt=zoom1x.png></b>&nbsp;means 1 bp is
    456 displayed by 1 pixel, whereas <b><img border=0 width=18 height=13
    457 src="manual_e.files/image023.jpg" alt=zoom01x.png></b>&nbsp;means 10 bp is
    458 displayed by 1 pixel. So <b><img border=0 width=18 height=13
    459 src="manual_e.files/image018.jpg" alt=zoom10x.png></b>&nbsp;means the scale
    460 that enlarges the display up to the base level.<span style='color:red'> </span><b><img
    461 border=0 width=18 height=13 src="manual_e.files/image024.jpg"
    462 alt=zoom0001x.png></b><span style='color:red'>&nbsp;</span>is a scale ratio
    463 useful in displaying 1M bps on the screen.<span style='color:red'> </span>&nbsp;At
    464 the time of scaling up or down the view points of the present display will be
    465 remained unchanged.<span style='color:red'> </span></span></p>
    466 
    467 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    468 
    469 <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Using
    470 overview, ruler and zooming track method</span></h3>
    471 
    472 <p class=MsoNormal><span lang=EN-US>In addition, there are some methods to
    473 shifting. These are overview, ruler, zooming trucks. You can shift the
    474 viewpoint by clicking any position of these tracks. For details, please refer
    475 to the respective details about the each track.</span></p>
    476 
    477 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    478 
    479 <h2><span lang=EN-US>4.2. Functions of buttons</span></h2>
    480 
    481 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    482 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    483 </span></span><b><span lang=EN-US>(rev)&nbsp; </span></b><span lang=EN-US>You
    484 can display the sequence in reverse mode by UT Genome Browser. Normally a sequence
    485 is displayed from left to right but you can reverse it with the (rev) button. An
    486 alternative way to display in reverse way is to input “start” value greater
    487 than “end” value in the Input Box. The same task can be done easily by clicking
    488 the (rev) button. As the (rev) button reverses start and end points of the
    489 present displayed sequence so this can change the display mode from normal to
    490 reverse or vice versa.<b> </b>If you press the (fasta) button on reverse mode,
    491 then the complementary strand of displayed strand will be retrieved.</span></p>
    492 
    493 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    494 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    495 </span></span><b><span lang=EN-US>(top)&nbsp; </span></b><span lang=EN-US>By
    496 pressing this button you can return to the main screen. Information about
    497 present displayed range, track and each track setting etc. will be preserved.</span></p>
    498 
    499 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    500 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    501 </span></span><b><span lang=EN-US>(clear)&nbsp; </span></b><span lang=EN-US>By
    502 pressing this button you can return to the main screen. Information about
    503 present displayed range, track and each track setting etc. will be initialized.&nbsp;&nbsp;
    504 </span></p>
    505 
    506 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    507 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    508 </span></span><b><span lang=EN-US>(Track)&nbsp; </span></b><span lang=EN-US>Addition,
    509 deletion, and rearranging can be performed by this button. Details description
    510 will be given later.</span></p>
    511 
    512 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    513 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    514 </span></span><b><span lang=EN-US>(fasta)&nbsp; </span></b><span lang=EN-US>Present
    515 displaying sequence can be retrieved with this button in fasta format. You will
    516 be instructed to save as a file name. For example,<b> </b>Medaka-200406-scaffold429
    517 (64587-66612). fasta</span></p>
    518 
    519 <p class=MsoNormal><span lang=EN-US style='color:red'>&nbsp;</span></p>
    520 
    521 <h2><span lang=EN-US>4.3. Addition, Deletion, and Rearrangement of Tracks</span></h2>
    522 
    523 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    524 border=0 width=348 height=320 src="manual_e.files/image025.jpg"
    525 alt="browser_track.png"></span></p>
    526 
    527 <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>&nbsp;</span></b></p>
    528 
    529 <p class=MsoNormal><span lang=EN-US>When the (track) button of the main screen
    530 is pressed, the above track-editing screen will pop up. Here you can do addition,
    531 deletion and rearrangement of the tracks. This editing screen can be divided
    532 into three parts - displaying tracks, removed tracks, and adding new track.</span></p>
    533 
    534 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    535 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    536 </span></span><b><span lang=EN-US>Displaying track: </span></b><span
    537 lang=EN-US>Here, tracks’ deletion and rearrangement can be done to the present
    538 displayed screen. The deleted tracks will be replaced to next removed track. </span></p>
    539 
    540 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    541 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    542 </span></span><b><span lang=EN-US>Removed track: </span></b><span lang=EN-US>This
    543 is the list of all tracks, which are deleted at Displaying Tracks. It is something
    544 like garbage bin. Undo-processing is possible for the tracks that are displayed
    545 here.</span></p>
    546 
    547 <p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
    548 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    549 </span></span><b><span lang=EN-US>Add new track: </span></b><span lang=EN-US>New
    550 tracks, which are not available at present display, can be added by this track.
    551 By setting the URL of the new tracks, push add button. If the new tracks’ URL
    552 is read properly, the new tracks will be added after the present displayed
    553 tracks.&nbsp; </span></p>
    554 
    555 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    556 
    557 <h2><span lang=EN-US>4.4. Setting for Tracks</span></h2>
    558 
    559 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    560 border=0 width=358 height=288 src="manual_e.files/image026.jpg"></span></p>
    561 
    562 <p class=MsoNormal><span lang=EN-US>On main screen, when the <img border=0
    563 width=9 height=9 src="manual_e.files/image027.jpg" alt=cfg.png>&nbsp;button,
    564 beside the track name, is pressed, the display of that track can be customized
    565 as above image. The customizing contents of the tracks differ from each other.
    566 On the other hand, there are some tracks which contents cannot be customized at
    567 all. For details, please refer to the individual tracks information.&nbsp;&nbsp;
    568 </span></p>
    569 
    570 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    571 
    572 <h1><span lang=EN-US>5. Pre-defined Tracks</span></h1>
    573 
    574 <h2><span lang=EN-US>5.1. Overview Track</span></h2>
    575 
    576 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    577 border=0 width=552 height=15 src="manual_e.files/image028.jpg"
    578 alt="track_overview.png"></span></p>
    579 
    580 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
    581 style='font-size:12.0pt;font-family:"ＭＳ 明朝"'>&nbsp;</span></p>
    582 
    583 <p class=MsoNormal><span lang=EN-US>This track shows the range of present
    584 displayed window in the total genome. In above image, for instance, the
    585 blue-colored viewpoint shows the range from 125kb to 145kb. Clicking on any
    586 position of this overview track moves the viewpoint the middle position. For
    587 example, when you click on around 100k positions, the viewpoint will move to
    588 90k-110k. </span></p>
    589 
    590 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    591 
    592 <h2><span lang=EN-US>5.2. Ruler and Zooming Tracks</span></h2>
    593 
    594 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    595 border=0 width=566 height=9 src="manual_e.files/image029.jpg"></span></p>
    596 
    597 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    598 border=0 width=566 height=9 src="manual_e.files/image030.jpg"></span></p>
    599 
    600 <p class=MsoNormal><span lang=EN-US>Both the ruler track and the zooming track
    601 are displaying same contents with different color. These two show the base
    602 position number of the present displayed content with respect to the total
    603 sequence.&nbsp; If you click any position of the ruler track, the viewpoint
    604 will move to the middle position. For example, if the rightmost end of the
    605 ruler track is clicked then the same effect will be happed as the <img
    606 border=0 width=15 height=10 src="manual_e.files/image031.jpg" alt=ff.png>&nbsp;button
    607 of main screen is pressed. Before using the zoom button on main screen, it is
    608 better to have the required region on middle position by using the ruler track
    609 to smoothing future enlarge processing.</span></p>
    610 
    611 <p class=MsoNormal style='text-indent:5.25pt'><span lang=EN-US>In addition to
    612 the effect of the ruler track, if you click any position on the zooming track
    613 then two times zoom will be happened. For example, it is same to click the
    614 central button on zoom track as the <img border=0 width=13 height=13
    615 src="manual_e.files/image017.jpg" alt=zoomin.png>&nbsp;button on main screen.
    616 On the other hand, it is also same to clicking the rightmost end of the zooming
    617 track as click <img border=0 width=18 height=13
    618 src="manual_e.files/image014.jpg" alt=ff.png>&nbsp;then click <img border=0
    619 width=13 height=13 src="manual_e.files/image017.jpg" alt=zoomin.png>&nbsp;on
    620 main screen. This track is useful to zoom out our interested region on the
    621 sequence..</span></p>
    622 
    623 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    624 
    625 <h2><span lang=EN-US>5.3. Base Color Track</span></h2>
    626 
    627 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    628 border=0 width=566 height=9 src="manual_e.files/image032.jpg"><img border=0
    629 width=566 height=9 src="manual_e.files/image033.jpg"></span></p>
    630 
    631 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US>&nbsp;</span></p>
    632 
    633 <p class=MsoNormal><span lang=EN-US>Base color track changes the sequence to
    634 color mode. All four ATGC bases are displayed by converting to the individual color.
    635 It is natural to display each base pair by one pixel. By zooming in, you can
    636 see any specific region of the sequence in alphabet symbol (above bottom
    637 image). </span></p>
    638 
    639 <p class=MsoNormal style='text-indent:5.25pt'><span lang=EN-US>It is also possible
    640 to customize the corresponding base pair color also. For example, if GC base
    641 pair are only colored then we can use it as a simple GC content track. To get
    642 the sequence itself, it is better to save from fasta track.</span></p>
    643 
    644 <p class=MsoNormal><span lang=EN-US style='color:red'>&nbsp;</span></p>
    645 
    646 <h2><span lang=EN-US>5.4. Gap Track</span></h2>
    647 
    648 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    649 border=0 width=566 height=7 src="manual_e.files/image034.jpg"></span></p>
    650 
    651 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US>&nbsp;</span></p>
    652 
    653 <p class=MsoNormal><span lang=EN-US>Gap Track is a track that displays gaps in
    654 a scaffold. By clicking any place except the gap, we can get the whole contig
    655 sequence in FASTA format. It is different from the (fasta) button in the main
    656 window, because it does not retrieve the displayed sequence only, but saves the
    657 whole contig sequence.</span></p>
    658 
    659 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    660 
    661 <h2><span lang=EN-US>5.5. GC Content Track</span></h2>
    662 
    663 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    664 border=0 width=566 height=28 src="manual_e.files/image035.jpg"></span></p>
    665 
    666 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    667 
    668 <p class=MsoNormal><span lang=EN-US>This track displays the ratio of GC
    669 contents for 5 pixels. If the pixel number of a base pair is more than 5, the
    670 coloring will be done to tell whether it is GC or AT. </span></p>
    671 
    672 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    673 
    674 <h2><span lang=EN-US>5.6. Mapped Gene Track</span></h2>
    675 
    676 <p class=MsoNormal align=center style='margin-right:-60.8pt;text-align:center'><span
    677 lang=EN-US><img border=0 width=566 height=58 src="manual_e.files/image036.jpg"></span></p>
    678 
    679 <p class=MsoNormal style='margin-right:-60.8pt'><span lang=EN-US>&nbsp;</span></p>
    680 
    681 <p class=MsoNormal><span lang=EN-US>This track displays the mapping result of
    682 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
    683 mapping region for the gene is displayed by line and the exons are shown in rectangular
    684 box. The arrow sign shows the plus or minus strand of the genome. The above
    685 image displays Medaka’s ESTs in black color, while the green color indicates
    686 cDNAs of Fugu. The current data sources of mapped genes are Medaka Unigene
    687 Build#10, Zebra fish Unigene Build#71, and Fugu ensemble pufferfish v21.2.c1(
    688 10<sup>th</sup> May, 2004). We will revise the alignment periodically in
    689 response to the update of the data sources.</span></p>
    690 
    691 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    692 
    693 <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Display
    694 setting</span></h3>
    695 
    696 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    697 border=0 width=358 height=288 src="manual_e.files/image037.jpg"></span></p>
    698 
    699 <p class=MsoNormal><span lang=EN-US>If the <img border=0 width=9 height=9
    700 src="manual_e.files/image027.jpg" alt=cfg.png>&nbsp;button on the left side of
    701 Mapped Gene Track is pressed, the display setting windows will pop up. There
    702 are three parts of this setting; namely, changing the total display style,
    703 alternating the mapping results if a gene will be displayed or not, and modifying
    704 the color of a gene. The setting, whether to show or not, will display all
    705 which fulfill the conditions. The color setting can be done by “use this color”
    706 button beside the track.&nbsp; </span></p>
    707 
    708 <p class=MsoNormal><b><span lang=EN-US>Style select setting</span></b></p>
    709 
    710 <p class=MsoNormal><span lang=EN-US>Predicted genes’ display setting can be
    711 changed here. There are four kinds of display style. These styles are full,
    712 pack, small and dense. </span></p>
    713 
    714 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    715 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    716 </span></span><b><span lang=EN-US>Full:</span></b><span lang=EN-US> In full
    717 style, each gene’s position is displayed on one line. On left side the Genebank
    718 accession number or Ensemble Gene ID is written. <br>
    719 <img border=0 width=489 height=156 src="manual_e.files/image038.jpg"></span></p>
    720 
    721 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    722 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    723 </span></span><b><span lang=EN-US>Pack:</span></b><span lang=EN-US> By showing
    724 individual alignments together with the names (Genebank Acc or Ensemble Gene
    725 ID) of genes on left side in multiple on one line, the pack style is more
    726 compact than full style.<br>
    727 <img border=0 width=488 height=50 src="manual_e.files/image039.jpg"></span></p>
    728 
    729 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    730 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    731 </span></span><b><span lang=EN-US>Small:</span></b><span lang=EN-US> In small
    732 style, the up and down spaces for one gene are reduced to the minimum. Unlike
    733 the full style and the pack style, this does not display the names of the
    734 genes.<br>
    735 
    736 <img border=0 width=488 height=17 src="manual_e.files/image040.jpg"></span></p>
    737 
    738 <p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
    739 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    740 </span></span><b><span lang=EN-US>Dense:</span></b><span lang=EN-US> In this
    741 style, only the positions of aligned exons are displayed on one line.<br>
    742 <img border=0 width=484 height=8 src="manual_e.files/image041.jpg"></span></p>
    743 
    744 <p class=MsoNormal><span lang=EN-US>At present except the full style, if the
    745 numbers of the mapped genes are more than 200 in a range of more than 50kbp, the
    746 graphical view of the genes will be displayed.</span></p>
    747 
    748 <p class=MsoNormal><b><span lang=EN-US>FormSpecies disp setting</span></b></p>
    749 
    750 <p class=MsoNormal><span lang=EN-US>Here we can set which species among Medaka,
    751 Zebra fish, Fugu’s mapping results are displayed or not. On default, all
    752 species results will be displayed. Only the species, which are checked on the
    753 Checkbook, will be displayed.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>
    754 
    755 <p class=MsoNormal><b><span lang=EN-US>FromSpecies color setting </span></b></p>
    756 
    757 <p class=MsoNormal><span lang=EN-US>The color distinguishing for Medaka, Zebra
    758 fish, Fugu’s can be done here.</span></p>
    759 
    760 <p class=MsoNormal><b><span lang=EN-US>MatchRatio gradation setting</span></b></p>
    761 
    762 <p class=MsoNormal><span lang=EN-US>Gene’s color can be changed with respect to
    763 its match ratio. Provided colors for the match ratios 0.7 and 1.0 respectively,
    764 the system automatically gradates the coloring of the alignments between the
    765 lower and upper match ratios.&nbsp;&nbsp; </span></p>
    766 
    767 <p class=MsoNormal><b><span lang=EN-US>MatchRatio ulbound setting</span></b></p>
    768 
    769 <p class=MsoNormal><span lang=EN-US>You can specify the range of the mapping
    770 ratio by inputting the lower and upper bounds into the corresponding boxes.
    771 Alignments of match ratios within the range are only displayed.</span></p>
    772 
    773 <p class=MsoNormal><b><span lang=EN-US>CoverRatio gradation setting</span></b></p>
    774 
    775 <p class=MsoNormal><span lang=EN-US>Gene’s color can also be changed with
    776 respect to its cover ratio. Provided colors for the cover ratios 0.4 and 1.0
    777 respectively, the system automatically gradates the coloring of the alignments
    778 between the lower and upper cover ratios.&nbsp;&nbsp; </span></p>
    779 
    780 <p class=MsoNormal><b><span lang=EN-US>CoverRatio ulbound setting</span></b></p>
    781 
    782 <p class=MsoNormal><span lang=EN-US>You can specify the range of the cover
    783 ratio by inputting the lower and upper bounds into the corresponding boxes.
    784 Alignments of cover ratios within the range are only displayed.</span></p>
    785 
    786 <p class=MsoNormal><b><span lang=EN-US>Stage disp setting</span></b></p>
    787 
    788 <p class=MsoNormal><span lang=EN-US>Here, you can fix which development stage’s
    789 expression EST should be displayed.&nbsp; </span></p>
    790 
    791 <p class=MsoNormal><b><span lang=EN-US>Stage color setting</span></b></p>
    792 
    793 <p class=MsoNormal><span lang=EN-US>Color distinguishing can be done with
    794 respect to development stage.</span></p>
    795 
    796 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    797 
    798 <h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Linkage
    799 for each gene </span></h3>
    800 
    801 <p class=MsoNormal><span lang=EN-US>In full, pack and small style, each gene
    802 can be clicked on. By clicking each gene, you can see the details of this gene.</span></p>
    803 
    804 <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>&nbsp;</span></b></p>
    805 
    806 <h2><span lang=EN-US>5.7. Genscan Track</span></h2>
    807 
    808 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    809 border=0 width=567 height=39 src="manual_e.files/image042.jpg"></span></p>
    810 
    811 <p class=MsoNormal><span lang=EN-US>This track displays the predicted genes by
    812 Genscan. The predicted genes are viewed on lines, where the exons parts are on rectangular
    813 shape. Arrow sign presents the strand of the genes. The above image shows the
    814 predicted genes in pack style. </span></p>
    815 
    816 <p class=MsoNormal><b><span lang=EN-US>Display settings</span></b></p>
    817 
    818 <p class=MsoNormal><span lang=EN-US>If the <img border=0 width=9 height=9
    819 src="manual_e.files/image027.jpg" alt=cfg.png>&nbsp;mark button on the left
    820 side of Genscan Track is clicked, the display setting will pop up. Here are the
    821 details of this setting. </span></p>
    822 
    823 <p class=MsoNormal><b><span lang=EN-US>Style selects setting</span></b></p>
    824 
    825 <p class=MsoNormal><span lang=EN-US>Predicted genes’ display setting can be
    826 changed here. There are four kinds of display style. These styles are full,
    827 pack, small and dense, and they are similar to those styles in Mapped Gene
    828 Track.</span></p>
    829 
    830 <p class=MsoNormal><b><span lang=EN-US>Linkage of each gene</span></b></p>
    831 
    832 <p class=MsoNormal><span lang=EN-US>In full, pack and small style each gene can
    833 be clicked on. After clicking each gene, the details of prediction by Genscan
    834 will be appeared.</span></p>
    835 
    836 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    837 
    838 <h2><span lang=EN-US>5.8. Comparative Genomics Track</span></h2>
    839 
    840 <p class=MsoNormal><b><span lang=EN-US style='font-size:12.0pt'>Fugu Scaffold
    841 track</span></b></p>
    842 
    843 <p class=MsoNormal><b><span lang=EN-US>Description</span></b></p>
    844 
    845 <p class=MsoNormal><span lang=EN-US>This track shows Fugu/Medaka homologous
    846 scaffolds detected by ALPS alignment program. Fugu scaffolds are denoted by
    847 boxes connected by arrows. The boxes represent regions of high homology (match
    848 ratio &gt; 60%) aligned by ALPS. The arrows represent low homology regions or
    849 gaps in Fugu scaffold.&nbsp; The direction of arrows indicates the orientation
    850 of Fugu/Medaka alignments. Clicking on a Fugu scaffold will open a new window
    851 to display its dotplot with Fugu scaffold sequence provided in the same page.&nbsp;
    852 The Fugu sequence (Fugu v.2.0) was downloaded from JGI.</span></p>
    853 
    854 <p class=MsoNormal><b><span lang=EN-US>Method</span></b></p>
    855 
    856 <p class=MsoNormal><span lang=EN-US>Fugu scaffold sequences are split into
    857 non-overlapping 300mer sequences and these 300mer sequences are mapped to
    858 Medaka scaffolds with ALPS. ALPS alignments with match ratio less than 60% are
    859 discarded and remaining alignments are chained by longest monotone subsequence
    860 algorithm. Chains consist of more than 10 alignments are displayed in the
    861 track. Note that inversions or microrearrangements are not shown. Only the longest
    862 monotone subsequence is displayed for each Fugu scaffold.</span></p>
    863 
    864 <p class=MsoNormal><b><span lang=EN-US>Linkage of each scaffold </span></b></p>
    865 
    866 <p class=MsoNormal><span lang=EN-US>In full, pack and small style each gene can
    867 be clicked on. After clicking each scaffold, the detailed alignments will be
    868 appeared as like dot plot. Dotplot shows homologous regions of Fugu/Medaka
    869 scaffolds as diagonal runs of dots. Each dot, plotted based on sequence
    870 similarity score, indicates that significantly many seed matches are found
    871 between corresponding regions. The sequence similarity score is defined in such
    872 a way that tandem repeats are not assigned high scores while unique sequences
    873 are assigned high scores.</span></p>
    874 
    875 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
    876 border=0 width=567 height=201 src="manual_e.files/image043.jpg"></span></p>
    877 
    878 <p class=MsoNormal align=center style='text-align:center'><span lang=EN-US>&nbsp;</span></p>
    879 
    880 <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US>&nbsp;</span></b></p>
    881 
    882 <span lang=EN-US style='font-size:10.5pt;font-family:Century'><br clear=all
    883 style='page-break-before:always'>
    884 
    885 </span>
    886 
    887 <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>Ramen Assembler
    888 / UT Genome Browser Team Members</span></b></p>
    889 
    890 <p class=MsoNormal><span lang=EN-US><br>
    891 Ramen Genome Assembler Development Team</span></p>
    892 
    893 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    894 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    895 </span></span><span lang=EN-US>Development of “Ramen” genome assembler and
    896 assembly of medaka genome:<br>
    897 Masahiro Kasahara and Shin Sasaki</span></p>
    898 
    899 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    900 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    901 </span></span><span lang=EN-US>Development of “Ramen Viewer” for genome
    902 assembly: <br>
    903 
    904 Yukinobu Nagayasu</span></p>
    905 
    906 <p class=MsoNormal><span lang=EN-US><br>
    907 UT Genome Browser Development Team</span></p>
    908 
    909 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    910 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    911 </span></span><span lang=EN-US>Design and development of UT Genome Browser,
    912 keyword search function, libraries for describing tracks: <br>
    913 Yukinobu Nagayasu and Koichiro Doi</span></p>
    914 
    915 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    916 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    917 </span></span><span lang=EN-US>Online mapping function for query sequences:<br>
    918 Tomoyuki Yamada</span></p>
    919 
    920 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    921 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    922 </span></span><span lang=EN-US>Comparative Genomics Track:<br>
    923 Yoichiro Nakatani and Wei Qu</span></p>
    924 
    925 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    926 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    927 </span></span><span lang=EN-US>Gene Prediction:<br>
    928 Ahsan Budrul</span></p>
    929 
    930 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    931 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    932 </span></span><span lang=EN-US>Mapped Gene Track:<br>
    933 Yasuhiro Kasai</span></p>
    934 
    935 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    936 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    937 </span></span><span lang=EN-US>Database access accelerators:<br>
    938 Takehiro Furudate and Atsushi Mori</span></p>
    939 
    940 <p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
    941 lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    942 </span></span><span lang=EN-US>Overall management:<br>
    943 Koichiro Doi and Shinichi Morishita</span></p>
    944 
    945 <p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>
    946 
    947 <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>Acknowledgements</span></b></p>
    948 
    949 <p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>&nbsp;</span></b></p>
    950 
    951 <p class=MsoNormal><span lang=EN-US>This work has been supported by
    952 Grant-in-Aid for Scientific Research on Priority Areas (Grant#12209003) to
    953 Shinichi Morishita. </span></p>
    954 
    955 <p class=MsoNormal><span lang=EN-US>Ramen Assembler Development Team members
    956 are indebted to Yuji Kohara and Tadasu Shin-i for their technical discussions
    957 on the whole genome shotgun assembly.</span></p>
    958 
    959 <p class=MsoNormal><span lang=EN-US>Members in the UT Genome Browser
    960 Development Team are grateful to Kiyoshi Naruse, Daisuke Kobayashi, and
    961 Takanori Narita for their valuable input to improve the functions of the
    962 browser in a variety of ways.</span></p>
    963 
    964 </div>
    965 }}}
     2
     31. Welcome
     4
     5Welcome 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.
     6
     7ü         You can search gene, by gene name, clone name, cluster name and display its surroundings gene groups.
     8
     9ü         You can map a genomic sequence to any genome and observe its surroundings.
     10
     11ü         You can save the sequence itself on your system from here.
     12
     13Questions, suggestions or comments are welcome to webmaster@utgenome.org.
     14
     15 
     162. Keyword Search
     17
     18keyword_top.png
     19
     20 
     21
     22The 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.)
     23
     24 
     252.1. Gene List
     26
     27keyword_genes.png
     28
     29 
     30
     31When there are many genes for one keyword search, all genes will be displayed on a list. Pressing the (*) button on the left side, you can go to the mapped region for the gene. This list appears when multiple candidate entries are found, typically when class names or part of a gene number are input as a keyword. If a Genebank accession number is given, the number must be unique, and hence this list does not appear.
     32
     33 
     342.2. Mapping Position List
     35
     36keyword_locs.png
     37
     38 
     39
     40If the query gene has mapped to several regions on the genomic sequence, the list of all positions will be shown. Pressing the (*) button on the left side displays the mapped region of the gene. If there is only one mapped region of the gene, the list is skipped to display.
     41
     42 
     433. Sequence Alignment
     44
     45online01.PNG
     46
     47 
     48
     49Sequence mapping is possible by inputting a sequence in the online mapping frame (above image) at the bottom of the main window. After selecting the species and its revision, press the search button on the bottom. The request is sent to the alignment server ALPS to align the given sequence to the selected genome. Afterwards, the list of alignment results is returned if the system finds some alignments.
     50
     51 
     52
     53online02.PNG
     54
     55From the list, you can select one alignment by clicking the result button as illustrated above. Then, the aligned result will appear on the browser. The ALPS mapping track in following snapshot displays the added mapping status.
     56
     57 
     58
     59online03.PNG
     604. Main Window
     61
     62browser_main.png
     63
     64 
     65
     66The above picture shows the main screen for UT Genome Browser. It is possible to see the targeted region of genomic sequence by many tracks. This browser provides the following functions to manipulate tracks on this image screen.
     67
     68ü         Shifting, zooming in and out, and reversing of the target region. It facilitates zooming in the sequence until bases can be seen, while providing a panoramic, structural view for the sequence.
     69
     70ü         Adding, deleting and reordering the tracks.
     71
     72ü         Customizing of each track’s display.
     73
     74ü         Retrieving the present displayed sequence in Fasta format.
     75
     76ü         Continuing keyword search.
     77
     78In what follows, we describe the detail about each function.
     79
     80 
     814.1   Scrolling and zooming the main window
     82
     83On main window, it is possible to shift and to zoom in/out the present observing sequence. These tasks can be carried out by:
     84
     85ü         Inputting value in the input box method.
     86
     87ü         Using shifting button method.
     88
     89ü         Using overview, ruler and zooming track method.
     90
     91 
     92Inputting value in the input box method
     93
     94browser_params.png
     95
     96You can input values into the input boxes (like above image) inside the main window. The details about this method are as follows,
     97
     98ü         Species: Select the species to display. The selectable revisions would be changed with respect to the species. At present, only Medaka is possible to be selected.
     99
     100ü         Revision: Select the revision of the target specie’s genome. For Medaka, the revision name format is yyyymm. The selecting topics will change with respect to the selected revision.
     101
     102ü         Target: Select the target region to be displayed, from the selected species and selected revision. In the case of 200406 revision of Medaka, only scaffold name (e.g. scaffold123) can be selected but not the chromosome name (e.g. chr10). Chromosome numbers will be available in our later revision.
     103
     104ü         Start: Select the start position from your targeted sequence to display. The number should be 1-origin (i.e. the starting point will be 1).
     105
     106ü         End: Select the end point from your targeted sequence to display. The number should be 1-origin. If the ending point is greater than the starting point then the display will be normal. Otherwise, the display will be reverse. In both cases, the ending base will be included in the displaying sequence.
     107
     108ü         Width: Input the width in terms of pixels for output track display. Input the value that is suitable for your vision. Normally, it is assumed that width is equal to the screen width. It is also possible to input the width as 10 times bigger than the screen width. In that case, it seems to be convenient to use the scroll of the browser.
     109
     110After manipulating the previous items, press the “Apply” button to shifting to the desired position of the sequence.
     111
     112 
     113Using shifting button method
     114
     115browser_moves.png
     116
     117Moreover, there is another method by using the button (like above image). Normally, the input box method is useful only when it is important to have the correct position of the sequence.  As number must be supplied in this method, sometime this process is quit cumbersome. So we provide more intuitive methods for your convenience. So the buttons related to these methods are as follows,
     118
     119ü         Shifting (rr.png,r.png,f.png,ff.png):  rr.png,r.png,f.png,ff.png are buttons to shifting the sequence. Therr.png button scrolls sequence up to one screen size where the r.png button scrolls half screen to the left. The inverse buttons are for shifting to the right. 
     120
     121ü         Scaling (zoomout.png, zoomin.png, zoom10x.png, zoom1x.png, zoom01x.png, zoom001x.png, zoom0001x.png):  The zoomout.png button does scaling down and the display will be half of the present size where zoomin.png button does scaling up and the display will be 2 times bigger than present size. The fractional form button specifies the scale directly. The scaling unit is 1bp/pixel. For example, zoom1x.png means 1 bp is displayed by 1 pixel, whereas zoom01x.png means 10 bp is displayed by 1 pixel. So zoom10x.png means the scale that enlarges the display up to the base level. zoom0001x.png is a scale ratio useful in displaying 1M bps on the screen.  At the time of scaling up or down the view points of the present display will be remained unchanged.
     122
     123 
     124Using overview, ruler and zooming track method
     125
     126In 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.
     127
     128 
     1294.2. Functions of buttons
     130
     131ü         (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.
     132
     133ü         (top)  By pressing this button you can return to the main screen. Information about present displayed range, track and each track setting etc. will be preserved.
     134
     135ü         (clear)  By pressing this button you can return to the main screen. Information about present displayed range, track and each track setting etc. will be initialized. 
     136
     137ü         (Track)  Addition, deletion, and rearranging can be performed by this button. Details description will be given later.
     138
     139ü         (fasta)  Present displaying sequence can be retrieved with this button in fasta format. You will be instructed to save as a file name. For example, Medaka-200406-scaffold429 (64587-66612). fasta
     140
     141 
     1424.3. Addition, Deletion, and Rearrangement of Tracks
     143
     144browser_track.png
     145
     146 
     147
     148When the (track) button of the main screen is pressed, the above track-editing screen will pop up. Here you can do addition, deletion and rearrangement of the tracks. This editing screen can be divided into three parts - displaying tracks, removed tracks, and adding new track.
     149
     150ü         Displaying track: Here, tracks’ deletion and rearrangement can be done to the present displayed screen. The deleted tracks will be replaced to next removed track.
     151
     152ü         Removed track: This is the list of all tracks, which are deleted at Displaying Tracks. It is something like garbage bin. Undo-processing is possible for the tracks that are displayed here.
     153
     154ü         Add new track: New tracks, which are not available at present display, can be added by this track. By setting the URL of the new tracks, push add button. If the new tracks’ URL is read properly, the new tracks will be added after the present displayed tracks.
     155
     156 
     1574.4. Setting for Tracks
     158
     159On 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. 
     160
     161 
     1625. Pre-defined Tracks
     1635.1. Overview Track
     164
     165track_overview.png
     166
     167 
     168
     169This 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.
     170
     171 
     1725.2. Ruler and Zooming Tracks
     173
     174Both 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.
     175
     176In 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..
     177
     178 
     1795.3. Base Color Track
     180
     181 
     182
     183Base 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).
     184
     185It 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.
     186
     187 
     1885.4. Gap Track
     189
     190 
     191
     192Gap Track is a track that displays gaps in a scaffold. By clicking any place except the gap, we can get the whole contig sequence in FASTA format. It is different from the (fasta) button in the main window, because it does not retrieve the displayed sequence only, but saves the whole contig sequence.
     193
     194 
     1955.5. GC Content Track
     196
     197 
     198
     199This 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.
     200
     201 
     2025.6. Mapped Gene Track
     203
     204 
     205
     206This 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.
     207
     208 
     209Display setting
     210
     211If the cfg.png button on the left side of Mapped Gene Track is pressed, the display setting windows will pop up. There are three parts of this setting; namely, changing the total display style, alternating the mapping results if a gene will be displayed or not, and modifying the color of a gene. The setting, whether to show or not, will display all which fulfill the conditions. The color setting can be done by “use this color” button beside the track.
     212
     213Style select setting
     214
     215Predicted genes’ display setting can be changed here. There are four kinds of display style. These styles are full, pack, small and dense.
     216
     217ü         Full: In full style, each gene’s position is displayed on one line. On left side the Genebank accession number or Ensemble Gene ID is written.
     218
     219ü         Pack: By showing individual alignments together with the names (Genebank Acc or Ensemble Gene ID) of genes on left side in multiple on one line, the pack style is more compact than full style.
     220
     221ü         Small: In small style, the up and down spaces for one gene are reduced to the minimum. Unlike the full style and the pack style, this does not display the names of the genes.
     222
     223ü         Dense: In this style, only the positions of aligned exons are displayed on one line.
     224
     225At present except the full style, if the numbers of the mapped genes are more than 200 in a range of more than 50kbp, the graphical view of the genes will be displayed.
     226
     227FormSpecies disp setting
     228
     229Here we can set which species among Medaka, Zebra fish, Fugu’s mapping results are displayed or not. On default, all species results will be displayed. Only the species, which are checked on the Checkbook, will be displayed.     
     230
     231FromSpecies color setting
     232
     233The color distinguishing for Medaka, Zebra fish, Fugu’s can be done here.
     234
     235MatchRatio gradation setting
     236
     237Gene’s color can be changed with respect to its match ratio. Provided colors for the match ratios 0.7 and 1.0 respectively, the system automatically gradates the coloring of the alignments between the lower and upper match ratios. 
     238
     239MatchRatio ulbound setting
     240
     241You can specify the range of the mapping ratio by inputting the lower and upper bounds into the corresponding boxes. Alignments of match ratios within the range are only displayed.
     242
     243CoverRatio gradation setting
     244
     245Gene’s color can also be changed with respect to its cover ratio. Provided colors for the cover ratios 0.4 and 1.0 respectively, the system automatically gradates the coloring of the alignments between the lower and upper cover ratios. 
     246
     247CoverRatio ulbound setting
     248
     249You can specify the range of the cover ratio by inputting the lower and upper bounds into the corresponding boxes. Alignments of cover ratios within the range are only displayed.
     250
     251Stage disp setting
     252
     253Here, you can fix which development stage’s expression EST should be displayed.
     254
     255Stage color setting
     256
     257Color distinguishing can be done with respect to development stage.
     258
     259 
     260Linkage for each gene
     261
     262In full, pack and small style, each gene can be clicked on. By clicking each gene, you can see the details of this gene.
     263
     264 
     2655.7. Genscan Track
     266
     267This 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.
     268
     269Display settings
     270
     271If 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.
     272
     273Style selects setting
     274
     275Predicted 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.
     276
     277Linkage of each gene
     278
     279In full, pack and small style each gene can be clicked on. After clicking each gene, the details of prediction by Genscan will be appeared.
     280
     281 
     2825.8. Comparative Genomics Track
     283
     284Fugu Scaffold track
     285
     286Description
     287
     288This 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.
     289
     290Method
     291
     292Fugu 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.
     293
     294Linkage of each scaffold
     295
     296In 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.
     297
     298 
     299
     300 
     301
     302Ramen Assembler / UT Genome Browser Team Members
     303
     304
     305Ramen Genome Assembler Development Team
     306
     307ü         Development of “Ramen” genome assembler and assembly of medaka genome:
     308Masahiro Kasahara and Shin Sasaki
     309
     310ü         Development of “Ramen Viewer” for genome assembly:
     311Yukinobu Nagayasu
     312
     313
     314UT Genome Browser Development Team
     315
     316ü         Design and development of UT Genome Browser, keyword search function, libraries for describing tracks:
     317Yukinobu Nagayasu and Koichiro Doi
     318
     319ü         Online mapping function for query sequences:
     320Tomoyuki Yamada
     321
     322ü         Comparative Genomics Track:
     323Yoichiro Nakatani and Wei Qu
     324
     325ü         Gene Prediction:
     326Ahsan Budrul
     327
     328ü         Mapped Gene Track:
     329Yasuhiro Kasai
     330
     331ü         Database access accelerators:
     332Takehiro Furudate and Atsushi Mori
     333
     334ü         Overall management:
     335Koichiro Doi and Shinichi Morishita
     336
     337 
     338
     339Acknowledgements
     340
     341 
     342
     343This work has been supported by Grant-in-Aid for Scientific Research on Priority Areas (Grant#12209003) to Shinichi Morishita.
     344
     345Ramen Assembler Development Team members are indebted to Yuji Kohara and Tadasu Shin-i for their technical discussions on the whole genome shotgun assembly.
     346
     347Members in the UT Genome Browser Development Team are grateful to Kiyoshi Naruse, Daisuke Kobayashi, and Takanori Narita for their valuable input to improve the functions of the browser in a variety of ways.