= UTGB Manual =
{{{
#!html
<style>


<div class=Section1 style='layout-grid:18.0pt'>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
24.0pt'>&nbsp;</span></h1>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
24.0pt'>&nbsp;</span></h1>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
36.0pt'>UT Genome Browser</span></h1>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
36.0pt'>&nbsp;</span></h1>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
36.0pt'>User’s Manual</span></h1>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
36.0pt'>Version 1.0</span></h1>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
24.0pt'>&nbsp;</span></h1>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal align=center style='text-align:center'><b><span
 lang=EN-US style='font-size:24.0pt'>August 17, 2004</span></b></p>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
24.0pt'>&nbsp;</span></h1>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
22.0pt'>UT Genome Browser Development Team</span></h1>

<h1 align=center style='text-align:center'><span lang=EN-US style='font-size:
22.0pt'>&nbsp;</span></h1>

<b><span lang=EN-US style='font-size:18.0pt;font-family:Century'><br clear=all
style='page-break-before:always'>
</span></b>

<h1><span lang=EN-US>Table of Contents</span></h1>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>1<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Welcome</span></b></p>

<p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Keyword
Search</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2.1<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Gene List</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>2.2<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Mapping Position List</span></b></p>

<p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>3<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Online
Sequence Alignment</span></b></p>

<p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

</span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Main
Window</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.1<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Scrolling and Zooming the
Main Window</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.2<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Functions of Buttons</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.3<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Addition, Deletion, and
Rearrangement of Tracks</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>4.4<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Setting for Tracks</span></b></p>

<p class=MsoNormal style='margin-left:21.25pt;text-indent:-21.25pt;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></b><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>Pre-defined
Tracks</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.1<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Overview Tracks</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.2<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Ruler and Zooming Tracks</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.3<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Base Color Track</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.4<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Gap Track</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.5<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>GC Content Track</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.6<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Mapped Gene Track</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.7<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Genscan Track</span></b></p>

<p class=MsoNormal style='margin-left:49.6pt;text-indent:-10.0mm;line-height:
150%'><b><span lang=EN-US style='font-size:14.0pt;line-height:150%'>5.8<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></b><b><span
lang=EN-US style='font-size:14.0pt;line-height:150%'>Comparative Genomics Track</span></b></p>

<p class=MsoNormal style='line-height:150%'><b><span lang=EN-US
style='font-size:14.0pt;line-height:150%'>Ramen Assembler / UT Genome Browser
Team Members</span></b></p>

<p class=MsoNormal style='line-height:150%'><b><span lang=EN-US
style='font-size:14.0pt;line-height:150%'>Acknowledgements</span></b></p>

<span lang=EN-US style='font-size:10.5pt;line-height:150%;font-family:Century'><br
clear=all style='page-break-before:always'>
</span>

<p class=MsoNormal style='line-height:150%'><span class=a><span lang=EN-US
style='font-size:18.0pt;line-height:150%'>1. Welcome</span></span></p>

<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
of a target species (at present Medaka only) from several aspects. For example,
the following tasks can be performed with different combinations. </span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>You can search gene, by gene name, clone name,
cluster name and display its surroundings gene groups.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>You can map a genomic sequence to any genome and
observe its surroundings.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>You can save the sequence itself on your system
from here.</span></p>

<p class=MsoNormal><span lang=EN-US>Questions, suggestions or comments are
welcome to <a href="mailto:webmaster@utgenome.org">webmaster@utgenome.org</a>.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h1><span lang=EN-US>2. Keyword Search </span></h1>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=254 height=262 src="manual_e.files/image001.jpg"
alt="keyword_top.png"></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>The top window displays the keyword search
engine, as above picture illustrates. Inputting any keyword at the query box, we
can see the detail information about the query. More about keyword search can
be found in the help, written on the same window. In addition, if the keyword
is a part of targets, then all the targets will be displayed. For example, the
keyword “BCD” will match to “ABCD”, “BCDE”, “BCD” and “BCDF” etc. (this is
worked out with using a suffix array.)</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>2.1. Gene List</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=288 height=235 src="manual_e.files/image002.jpg"
alt="keyword_genes.png"></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>When 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.&nbsp; </span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>2.2. Mapping Position List</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=384 height=230 src="manual_e.files/image003.jpg"
alt="keyword_locs.png"></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>If 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.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h1><span lang=EN-US>3. Sequence Alignment </span></h1>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=408 height=195 src="manual_e.files/image004.jpg"
alt=online01.PNG></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>Sequence 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.</span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=353 height=431 src="manual_e.files/image005.jpg"></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=400 height=81 src="manual_e.files/image006.jpg"
alt=online02.PNG></span></p>

<p class=MsoNormal><span lang=EN-US>From 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.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=566 height=149 src="manual_e.files/image007.jpg"
alt=online03.PNG></span></p>

<h1><span lang=EN-US>4. Main Window</span></h1>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=509 height=324 src="manual_e.files/image008.jpg"
alt="browser_main.png"></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>The 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.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>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.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Adding, deleting and reordering the tracks.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Customizing of each track’s display.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Retrieving the present displayed sequence in Fasta
format.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Continuing keyword search.</span></p>

<p class=MsoNormal><span lang=EN-US>In what follows, we describe the detail
about each function.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>4.1&nbsp;&nbsp; Scrolling and zooming the main window </span></h2>

<p class=MsoNormal><span lang=EN-US>On main window, it is possible to shift and
to zoom in/out the present observing sequence. These tasks can be carried out
by:</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Inputting value in the input box method.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Using shifting button method.</span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Using overview, ruler and zooming track method.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Inputting
value in the input box method</span></h3>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=552 height=31 src="manual_e.files/image009.jpg"
alt="browser_params.png"></span></p>

<p class=MsoNormal><span lang=EN-US>You can input values into the input boxes
(like above image) inside the main window. The details about this method are as
follows,</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Species: </span></b><span lang=EN-US>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.</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Revision</span></b><span lang=EN-US>: 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.</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Target: </span></b><span lang=EN-US>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. </span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Start: </span></b><span lang=EN-US>Select the
start position from your targeted sequence to display. The number should be 1-origin
(i.e. the starting point will be 1).</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

</span></span><b><span lang=EN-US>End: </span></b><span lang=EN-US>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.</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Width: </span></b><span lang=EN-US>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.</span></p>

<p class=MsoNormal><span lang=EN-US>After manipulating the previous items,
press the “Apply” button to shifting to the desired position of the sequence.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Using
shifting button method</span></h3>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=267 height=25 src="manual_e.files/image010.jpg"
alt="browser_moves.png"></span></p>

<p class=MsoNormal><span lang=EN-US>Moreover, 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.&nbsp; 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,</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Shifting (</span></b><span lang=EN-US><img
border=0 width=18 height=13 src="manual_e.files/image011.jpg" alt=rr.png><b>,</b><img
border=0 width=13 height=13 src="manual_e.files/image012.jpg" alt=r.png><b>,</b><img
border=0 width=13 height=13 src="manual_e.files/image013.jpg" alt=f.png><b>,</b><img
border=0 width=18 height=13 src="manual_e.files/image014.jpg" alt=ff.png><b>):&nbsp;
</b><img border=0 width=18 height=13 src="manual_e.files/image011.jpg"
alt=rr.png><b>,</b><img border=0 width=13 height=13
src="manual_e.files/image012.jpg" alt=r.png><b>,</b><img border=0 width=13
height=13 src="manual_e.files/image013.jpg" alt=f.png><b>,</b><img border=0
width=18 height=13 src="manual_e.files/image015.jpg" alt=ff.png> are buttons to
shifting the sequence. The<img border=0 width=18 height=13
src="manual_e.files/image011.jpg" alt=rr.png> button scrolls sequence up to one
screen size where the <img border=0 width=13 height=13
src="manual_e.files/image012.jpg" alt=r.png>&nbsp;button scrolls half screen to
the left. The inverse buttons are for shifting to the right.&nbsp;&nbsp; </span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Scaling (<img border=0 width=13 height=13
src="manual_e.files/image016.jpg" alt=zoomout.png>, <img border=0 width=13
height=13 src="manual_e.files/image017.jpg" alt=zoomin.png>, <img border=0
width=18 height=13 src="manual_e.files/image018.jpg" alt=zoom10x.png>, <img
border=0 width=18 height=13 src="manual_e.files/image019.jpg" alt=zoom1x.png>, <img
border=0 width=18 height=13 src="manual_e.files/image020.jpg" alt=zoom01x.png>,
<img border=0 width=18 height=13 src="manual_e.files/image021.jpg"
alt=zoom001x.png>, <img border=0 width=18 height=13
src="manual_e.files/image022.jpg" alt=zoom0001x.png>):&nbsp; </span></b><span
lang=EN-US>The <b><img border=0 width=13 height=13
src="manual_e.files/image016.jpg" alt=zoomout.png></b>&nbsp;button does scaling
down and the display will be half of the present size where <b><img border=0
width=13 height=13 src="manual_e.files/image017.jpg" alt=zoomin.png></b>&nbsp;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, <b><img border=0 width=18 height=13
src="manual_e.files/image019.jpg" alt=zoom1x.png></b>&nbsp;means 1 bp is
displayed by 1 pixel, whereas <b><img border=0 width=18 height=13
src="manual_e.files/image023.jpg" alt=zoom01x.png></b>&nbsp;means 10 bp is
displayed by 1 pixel. So <b><img border=0 width=18 height=13
src="manual_e.files/image018.jpg" alt=zoom10x.png></b>&nbsp;means the scale
that enlarges the display up to the base level.<span style='color:red'> </span><b><img
border=0 width=18 height=13 src="manual_e.files/image024.jpg"
alt=zoom0001x.png></b><span style='color:red'>&nbsp;</span>is a scale ratio
useful in displaying 1M bps on the screen.<span style='color:red'> </span>&nbsp;At
the time of scaling up or down the view points of the present display will be
remained unchanged.<span style='color:red'> </span></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Using
overview, ruler and zooming track method</span></h3>

<p class=MsoNormal><span lang=EN-US>In addition, there are some methods to
shifting. These are overview, ruler, zooming trucks. You can shift the
viewpoint by clicking any position of these tracks. For details, please refer
to the respective details about the each track.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>4.2. Functions of buttons</span></h2>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>(rev)&nbsp; </span></b><span lang=EN-US>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.<b> </b>If you press the (fasta) button on reverse mode,
then the complementary strand of displayed strand will be retrieved.</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>(top)&nbsp; </span></b><span lang=EN-US>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.</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>(clear)&nbsp; </span></b><span lang=EN-US>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.&nbsp;&nbsp;
</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>(Track)&nbsp; </span></b><span lang=EN-US>Addition,
deletion, and rearranging can be performed by this button. Details description
will be given later.</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>(fasta)&nbsp; </span></b><span lang=EN-US>Present
displaying sequence can be retrieved with this button in fasta format. You will
be instructed to save as a file name. For example,<b> </b>Medaka-200406-scaffold429
(64587-66612). fasta</span></p>

<p class=MsoNormal><span lang=EN-US style='color:red'>&nbsp;</span></p>

<h2><span lang=EN-US>4.3. Addition, Deletion, and Rearrangement of Tracks</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=348 height=320 src="manual_e.files/image025.jpg"
alt="browser_track.png"></span></p>

<p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>&nbsp;</span></b></p>

<p class=MsoNormal><span lang=EN-US>When 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.</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Displaying track: </span></b><span
lang=EN-US>Here, tracks’ deletion and rearrangement can be done to the present
displayed screen. The deleted tracks will be replaced to next removed track. </span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Removed track: </span></b><span lang=EN-US>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.</span></p>

<p class=MsoNormal style='margin-left:31.5pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Add new track: </span></b><span lang=EN-US>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.&nbsp; </span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>4.4. Setting for Tracks</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=358 height=288 src="manual_e.files/image026.jpg"></span></p>

<p class=MsoNormal><span lang=EN-US>On main screen, when the <img border=0
width=9 height=9 src="manual_e.files/image027.jpg" alt=cfg.png>&nbsp;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.&nbsp;&nbsp;
</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h1><span lang=EN-US>5. Pre-defined Tracks</span></h1>

<h2><span lang=EN-US>5.1. Overview Track</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=552 height=15 src="manual_e.files/image028.jpg"
alt="track_overview.png"></span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US
style='font-size:12.0pt;font-family:"ＭＳ 明朝"'>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>This track shows the range of present
displayed window in the total genome. In above image, for instance, the
blue-colored viewpoint shows the range from 125kb to 145kb. Clicking on any
position of this overview track moves the viewpoint the middle position. For
example, when you click on around 100k positions, the viewpoint will move to
90k-110k. </span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>5.2. Ruler and Zooming Tracks</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=566 height=9 src="manual_e.files/image029.jpg"></span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=566 height=9 src="manual_e.files/image030.jpg"></span></p>

<p class=MsoNormal><span lang=EN-US>Both the ruler track and the zooming track
are displaying same contents with different color. These two show the base
position number of the present displayed content with respect to the total
sequence.&nbsp; 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 <img
border=0 width=15 height=10 src="manual_e.files/image031.jpg" alt=ff.png>&nbsp;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.</span></p>

<p class=MsoNormal style='text-indent:5.25pt'><span lang=EN-US>In addition to
the effect of the ruler track, if you click any position on the zooming track
then two times zoom will be happened. For example, it is same to click the
central button on zoom track as the <img border=0 width=13 height=13
src="manual_e.files/image017.jpg" alt=zoomin.png>&nbsp;button on main screen.
On the other hand, it is also same to clicking the rightmost end of the zooming
track as click <img border=0 width=18 height=13
src="manual_e.files/image014.jpg" alt=ff.png>&nbsp;then click <img border=0
width=13 height=13 src="manual_e.files/image017.jpg" alt=zoomin.png>&nbsp;on
main screen. This track is useful to zoom out our interested region on the
sequence..</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>5.3. Base Color Track</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=566 height=9 src="manual_e.files/image032.jpg"><img border=0
width=566 height=9 src="manual_e.files/image033.jpg"></span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>Base color track changes the sequence to
color mode. All four ATGC bases are displayed by converting to the individual color.
It is natural to display each base pair by one pixel. By zooming in, you can
see any specific region of the sequence in alphabet symbol (above bottom
image). </span></p>

<p class=MsoNormal style='text-indent:5.25pt'><span lang=EN-US>It is also possible
to customize the corresponding base pair color also. For example, if GC base
pair are only colored then we can use it as a simple GC content track. To get
the sequence itself, it is better to save from fasta track.</span></p>

<p class=MsoNormal><span lang=EN-US style='color:red'>&nbsp;</span></p>

<h2><span lang=EN-US>5.4. Gap Track</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=566 height=7 src="manual_e.files/image034.jpg"></span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>Gap 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.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>5.5. GC Content Track</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=566 height=28 src="manual_e.files/image035.jpg"></span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>This track displays the ratio of GC
contents for 5 pixels. If the pixel number of a base pair is more than 5, the
coloring will be done to tell whether it is GC or AT. </span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>5.6. Mapped Gene Track</span></h2>

<p class=MsoNormal align=center style='margin-right:-60.8pt;text-align:center'><span
lang=EN-US><img border=0 width=566 height=58 src="manual_e.files/image036.jpg"></span></p>

<p class=MsoNormal style='margin-right:-60.8pt'><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><span lang=EN-US>This track displays the mapping result of
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
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(
10<sup>th</sup> May, 2004). We will revise the alignment periodically in
response to the update of the data sources.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Display
setting</span></h3>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=358 height=288 src="manual_e.files/image037.jpg"></span></p>

<p class=MsoNormal><span lang=EN-US>If the <img border=0 width=9 height=9
src="manual_e.files/image027.jpg" alt=cfg.png>&nbsp;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.&nbsp; </span></p>

<p class=MsoNormal><b><span lang=EN-US>Style select setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>Predicted genes’ display setting can be
changed here. There are four kinds of display style. These styles are full,
pack, small and dense. </span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Full:</span></b><span lang=EN-US> 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. <br>
<img border=0 width=489 height=156 src="manual_e.files/image038.jpg"></span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Pack:</span></b><span lang=EN-US> 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.<br>
<img border=0 width=488 height=50 src="manual_e.files/image039.jpg"></span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Small:</span></b><span lang=EN-US> 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.<br>

<img border=0 width=488 height=17 src="manual_e.files/image040.jpg"></span></p>

<p class=MsoNormal style='margin-left:42.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><b><span lang=EN-US>Dense:</span></b><span lang=EN-US> In this
style, only the positions of aligned exons are displayed on one line.<br>
<img border=0 width=484 height=8 src="manual_e.files/image041.jpg"></span></p>

<p class=MsoNormal><span lang=EN-US>At 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.</span></p>

<p class=MsoNormal><b><span lang=EN-US>FormSpecies disp setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>Here 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.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>

<p class=MsoNormal><b><span lang=EN-US>FromSpecies color setting </span></b></p>

<p class=MsoNormal><span lang=EN-US>The color distinguishing for Medaka, Zebra
fish, Fugu’s can be done here.</span></p>

<p class=MsoNormal><b><span lang=EN-US>MatchRatio gradation setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>Gene’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.&nbsp;&nbsp; </span></p>

<p class=MsoNormal><b><span lang=EN-US>MatchRatio ulbound setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>You 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.</span></p>

<p class=MsoNormal><b><span lang=EN-US>CoverRatio gradation setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>Gene’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.&nbsp;&nbsp; </span></p>

<p class=MsoNormal><b><span lang=EN-US>CoverRatio ulbound setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>You 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.</span></p>

<p class=MsoNormal><b><span lang=EN-US>Stage disp setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>Here, you can fix which development stage’s
expression EST should be displayed.&nbsp; </span></p>

<p class=MsoNormal><b><span lang=EN-US>Stage color setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>Color distinguishing can be done with
respect to development stage.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h3 style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US>Linkage
for each gene </span></h3>

<p class=MsoNormal><span lang=EN-US>In full, pack and small style, each gene
can be clicked on. By clicking each gene, you can see the details of this gene.</span></p>

<p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>&nbsp;</span></b></p>

<h2><span lang=EN-US>5.7. Genscan Track</span></h2>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=567 height=39 src="manual_e.files/image042.jpg"></span></p>

<p class=MsoNormal><span lang=EN-US>This track displays the predicted genes by
Genscan. The predicted genes are viewed on lines, where the exons parts are on rectangular
shape. Arrow sign presents the strand of the genes. The above image shows the
predicted genes in pack style. </span></p>

<p class=MsoNormal><b><span lang=EN-US>Display settings</span></b></p>

<p class=MsoNormal><span lang=EN-US>If the <img border=0 width=9 height=9
src="manual_e.files/image027.jpg" alt=cfg.png>&nbsp;mark button on the left
side of Genscan Track is clicked, the display setting will pop up. Here are the
details of this setting. </span></p>

<p class=MsoNormal><b><span lang=EN-US>Style selects setting</span></b></p>

<p class=MsoNormal><span lang=EN-US>Predicted genes’ display setting can be
changed here. There are four kinds of display style. These styles are full,
pack, small and dense, and they are similar to those styles in Mapped Gene
Track.</span></p>

<p class=MsoNormal><b><span lang=EN-US>Linkage of each gene</span></b></p>

<p class=MsoNormal><span lang=EN-US>In full, pack and small style each gene can
be clicked on. After clicking each gene, the details of prediction by Genscan
will be appeared.</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<h2><span lang=EN-US>5.8. Comparative Genomics Track</span></h2>

<p class=MsoNormal><b><span lang=EN-US style='font-size:12.0pt'>Fugu Scaffold
track</span></b></p>

<p class=MsoNormal><b><span lang=EN-US>Description</span></b></p>

<p class=MsoNormal><span lang=EN-US>This track shows Fugu/Medaka homologous
scaffolds detected by ALPS alignment program. Fugu scaffolds are denoted by
boxes connected by arrows. The boxes represent regions of high homology (match
ratio &gt; 60%) aligned by ALPS. The arrows represent low homology regions or
gaps in Fugu scaffold.&nbsp; 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.&nbsp;
The Fugu sequence (Fugu v.2.0) was downloaded from JGI.</span></p>

<p class=MsoNormal><b><span lang=EN-US>Method</span></b></p>

<p class=MsoNormal><span lang=EN-US>Fugu scaffold sequences are split into
non-overlapping 300mer sequences and these 300mer sequences are mapped to
Medaka scaffolds with ALPS. ALPS alignments with match ratio less than 60% are
discarded and remaining alignments are chained by longest monotone subsequence
algorithm. Chains consist of more than 10 alignments are displayed in the
track. Note that inversions or microrearrangements are not shown. Only the longest
monotone subsequence is displayed for each Fugu scaffold.</span></p>

<p class=MsoNormal><b><span lang=EN-US>Linkage of each scaffold </span></b></p>

<p class=MsoNormal><span lang=EN-US>In full, pack and small style each gene can
be clicked on. After clicking each scaffold, the detailed alignments will be
appeared as like dot plot. Dotplot shows homologous regions of Fugu/Medaka
scaffolds as diagonal runs of dots. Each dot, plotted based on sequence
similarity score, indicates that significantly many seed matches are found
between corresponding regions. The sequence similarity score is defined in such
a way that tandem repeats are not assigned high scores while unique sequences
are assigned high scores.</span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US><img
border=0 width=567 height=201 src="manual_e.files/image043.jpg"></span></p>

<p class=MsoNormal align=center style='text-align:center'><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US>&nbsp;</span></b></p>

<span lang=EN-US style='font-size:10.5pt;font-family:Century'><br clear=all
style='page-break-before:always'>

</span>

<p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>Ramen Assembler
/ UT Genome Browser Team Members</span></b></p>

<p class=MsoNormal><span lang=EN-US><br>
Ramen Genome Assembler Development Team</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Development of “Ramen” genome assembler and
assembly of medaka genome:<br>
Masahiro Kasahara and Shin Sasaki</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Development of “Ramen Viewer” for genome
assembly: <br>

Yukinobu Nagayasu</span></p>

<p class=MsoNormal><span lang=EN-US><br>
UT Genome Browser Development Team</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Design and development of UT Genome Browser,
keyword search function, libraries for describing tracks: <br>
Yukinobu Nagayasu and Koichiro Doi</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Online mapping function for query sequences:<br>
Tomoyuki Yamada</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Comparative Genomics Track:<br>
Yoichiro Nakatani and Wei Qu</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Gene Prediction:<br>
Ahsan Budrul</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Mapped Gene Track:<br>
Yasuhiro Kasai</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Database access accelerators:<br>
Takehiro Furudate and Atsushi Mori</span></p>

<p class=MsoNormal style='margin-left:21.0pt;text-indent:-21.0pt'><span
lang=EN-US style='font-family:Wingdings'>&uuml;<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><span lang=EN-US>Overall management:<br>
Koichiro Doi and Shinichi Morishita</span></p>

<p class=MsoNormal><span lang=EN-US>&nbsp;</span></p>

<p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>Acknowledgements</span></b></p>

<p class=MsoNormal><b><span lang=EN-US style='font-size:14.0pt'>&nbsp;</span></b></p>

<p class=MsoNormal><span lang=EN-US>This work has been supported by
Grant-in-Aid for Scientific Research on Priority Areas (Grant#12209003) to
Shinichi Morishita. </span></p>

<p class=MsoNormal><span lang=EN-US>Ramen Assembler Development Team members
are indebted to Yuji Kohara and Tadasu Shin-i for their technical discussions
on the whole genome shotgun assembly.</span></p>

<p class=MsoNormal><span lang=EN-US>Members 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.</span></p>

</div>
}}}