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the name of the glyph will give you copious documentation on all the
options the glyph recognizes.

<h3><a name="descriptions">1.3. Adding Descriptions to a Feature</a></h3>

<p>

By default, GBrowse will display the name of the feature above its
glyph provided that there is sufficient space to do this.  Optionally,
you can also attach some descriptive text to the feature.  This text
will be displayed below the feature, and can also be searched.

<p>

You can place descriptions, notes and other comments into the ninth
column of the GFF load file.  The example file <a
href="data_files/volvox_domains.gff3">volvox_domains.gff3</a> shows how this is done.
An excerpt from the top of the file looks like this:

<blockquote class="example"><pre>
ctgA example polypeptide_domain 11911 15561 . + . Name=m11;Note=kinase
ctgA example polypeptide_domain 13801 14007 . - . Name=m05;Note=helix loop helix
ctgA example polypeptide_domain 14731 17239 . - . Name=m14;Note=kinase
ctgA example polypeptide_domain 15396 16159 . + . Name=m03;Note=zinc finger
</pre></blockquote>

<p>

This defines several new features of type "polypeptide_domain".  The
ninth column, in addition to giving each of the motifs names adds a
"Note" attribute to each feature. As described earlier, each attribute
is a name=value pair separated by semicolons.

<p>

The attribute named <i>Note</i> is automatically displayed and made
searchable.  To see this work, add <a
href="data_files/volvox_domains.gff3">volvox_domains.gff3</a> to the volvox database
directory.  You can do this just by copying the file into
<b>/var/lib/gbrowse2/databases/volvox</b> so that the directory contains both
the original volvox_remarks.gff3 and the new volvox_domains.gff3 files.

<p>

To display this newly-loaded data set, open up volvox.conf and add the
following new stanza to the config file:

<blockquote class="example"><pre>
[Motifs]
feature      = polypeptide_domain
glyph        = span
height       = 5
description  = 1
key          = Example motifs
</pre></blockquote>

<p>

This defines a new track whose internal name is "Motifs."  The
corresponding feature type is "motif" and it uses the "span" glyph, a
graphic that displays a horizontal line capped by vertical endpoints.
The height is set to five pixels, and the human-readable key is set to
"Example motifs."  A new option, "description" is a flag that tells
GBrowse to display the Note attribute, if any.  Any non-zero value
means true.

<p>

After updating the configuration file, you will need to reload the
browser page and turn on the "Example motifs" checkbox below the main
image. The result is shown in Figure 4.

<blockquote class="center">
<img  style="border:solid;border-width:1px" src="figures/descriptions1.gif"><br>
<i>Figure 4: Showing the Notes attribute</i>
</blockquote>

<p>

A copy of this config file is also available for you to use in
<a href="conf_files/volvox2.conf">volvox2.conf</a>.

<p>

To show that GBrowse will search the notes for keyword matches, try
typing in "kinase."  You will be presented with a list of all the
motifs whose Note attribute contains the word "kinase."

<h3><a name="naming">1.4. Adjusting GBrowse Name Searches</a></h3>

<p>

GBrowse has a very flexible search feature.  You can type in the name
of a reference sequence, such as "ctgA", and it will display the
entire thing, or you can type in a range in the format
"ctgA:start..stop".  Try "ctgA:5000..8000" to see this at work.

<p>

In addition, GBrowse can search for features by name. Anything that
has a Name or Alias attribute in the GFF3 file can be searched for by
name. For example, try searching for "f10" or even "f1*".

The only drawback to this is that you may have name collisions. For
example, some research communities distinguish genes from their
products using differences in capitalization, for example hga
and HGA. However, GBrowse's searches are case insensitive. To
avoid name collisions, you can give each type of feature a distinctive
naming prefix, for example "Gene:hga" and "Protein:HGB".

<p>

To illustrate how this works, have a look at <a
href="data_files/volvox_geneproducts.gff3">volvox_geneproducts.gff3:</a>

<blockquote class="example"><pre>
ctgA example remark                             1000 2000 . . . Name=hga
ctgA example protein_coding_primary_transcript  1100 2000 . + . Name=Gene:hga
ctgA example polypeptide                        1200 1900 . + . Name=Protein:HGA
ctgA example protein_coding_primary_transcript  1600 3000 . - . Name=Gene:hgb
ctgA example polypeptide                        1800 2900 . - . Name=Protein:HGB

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[elegans_core]
description = Core C. elegans annotations
path        = elegans_core.conf
</pre></blockquote>

<p>

Confirm that you can browse the database.  Figure 28 is a picture of
the entire data set with all core tracks turned on.

<blockquote class="center">
<img  style="border:solid;border-width:1px" src="figures/third_party1.gif"><br>
<i>Figure 28:</i> The core <i>C. elegans</i> dataset.
</blockquote>


<p>

We will now add some third-party annotations to the display.  These
are contained in the files "elegans_acceptor.gff3",
"elegans_expression.gff3", "elefans_sts.gff3", "elegans_deletion.gff3", and
"elegans_repeats.gff3":

<p>

<table border="1" width="100%">
  <TR>
    <td>
	<a href="data_files/elegans_acceptor.gff3">elegans_acceptor.gff3</a>
    </td>
    <td>
	Annotations of <i>C. elegans</i> spliced leader acceptor sites.
    </td>
  </TR>
    
  <TR>
    <td>
	<a href="data_files/elegans_expression.gff3">elegans_expression.gff3</a>
    </td>
    <td>
	Positions assayed for gene expression level in <i>C. elegans</i>
	microarrays.
    </td>
  </TR>
    
  <TR>
    <td>
	<a href="data_files/elegans_sts.gff3">elegans_sts.gff3</a>
    </td>
    <td>
	Primer pairs available for the region produced by the
	<i>C. elegans</i> ORFeome project.
    </td>
  </TR>

  <TR>
    <td>
	<a href="data_files/elegans_deletion.gff3">elegans_deletion.gff3</a>
    </td>
    <td>
	Deletion endpoints from a targeted gene knockout project.
    </td>
  </TR>
    
  <TR>
    <td>
	<a href="data_files/elegans_repeats.gff3">elegans_repeats.gff3</a>
    </td>
    <td>
	Complex repetitive elements found using the RepeatMasker program.
    </td>
  </TR>
    
</table>

<p>

We can load each of these files to private storage located on the
server using the file upload feature.  Copy these five files to your
home directory where you can find them easily.  Go to the tab named
<b>Upload and Share Tracks</b> and choose the link marked "Add custom
track(s) [From a file]". When the upload button appears, press it,
select one of the annotation files, and then press the "Upload" button
to upload the file to the server.  The annotations contained in the
file should now appear on the display.  If you now do this for all
five of the annotation files, you will eventually get a display like
that shown in Figure 29.

<p>

<blockquote class="center">
<img  style="border:solid;border-width:1px" src="figures/third_party2.gif"><br>
<i>Figure 29:</i> After uploading five annotation files.
</blockquote>

<p>

<blockquote> NOTE: <i>This upload function works even if the gbrowse
you are uploading to is located on a remote server.  The uploaded
files are stored in a private directory on the server away from the
main data set.  Other users cannot see your data, unless you
explicitly share the track as described later.</i> </blockquote>

<p>

Although this display is functional, the tracks are fairly uniform in
appearance.  Fortunately, we can customize the uploaded files quite
easily. One way is to use the graphical configuration editor. Find the
"deletion:Allele" project track and click on the "?" next to its
name. This will bring up a graphical settings block as shown in Figure
30. Change the glyph to "triangle" and the fill and line colors to
"red". When you press the "Change" button the track will be updated
with the desired settings.

<blockquote class="center">
<img  style="border:solid;border-width:1px" src="figures/setting_popup.png"><br>
<i>Figure 30:</i>You can change the appearance of a custom track by
clicking on the "?" next to the track.
</blockquote>

This customization only takes place for the current user. If you share