Uploading Editing Deleting Downloading File Format Customizing Appearance Displaying Intensity Plots & Other Numeric Data Publishing

Adding Annotations to the Genome

You can upload your own list of sequence annotations to this page and view them in the context of the genome. Uploaded annotations will persist until you edit them or delete them. Your annotations are private and will not be seen by other individuals. If you choose to, you can publish your annotations and share them with your colleagues.

To upload annotations:

  1. Create a text file using the format described below. The file must be text only.
  2. Use the Browse... button to select the file.
  3. Press the Upload button to upload the file.

The browser should now show a line of text that identifies the date you uploaded this file, and links to the sequence(s) which you have annotated:

[your_file.txt] Last modified Mon Dec 17 08:43:36 2001. Annotated sequences: T22A3

From now on, whenever you browse a region covered by your annotations they will appear on the display. To quickly go to an annotated region, click on its link. (If your file contains too many annotated regions they will not be shown as individual links.)


To edit annotations:

Your annotations will persist until you delete them, or until they are not accessed for a long period of time, typically 60 days. To modify them, you can upload a new file, replacing the old one. Alternatively, you can edit them on-line.

  1. Press the Edit Data... button. This will display a text field containing your uploaded annotations.
  2. Make the changes you want.
  3. Press Submit Changes...

You can use the edit button to create an annotation file from scratch. Just type the annotation data into the text field or cut and paste from your favorite word processor.


To Download or Delete Annotations

  1. To delete your annotations, press the Delete Data button.
  2. To download your annotations as a text file, press the Download Data button.
  3. Turn the display of your annotations on and off by setting the Uploaded Annotations checkbox.
  4. Change the relative position of your annotations using the Set Track Options... button.

Annotation File Format

This browser accepts non-quantitative data in a simple but flexible format described here, and quantitative data using WIG format. For quantitative data (such as microarray expression levels), please use the UCSC Genome Browser's "WIG" format. For qualitative data, annotation files must be text only. Here is an example:

[mRNA]
glyph = gene
key   = My Genes

mRNA hox1 Chr1:1..100 Type=UTR
mRNA hox1 Chr1:101..200,300..400,500..800 Type=CDS
mRNA hox1 Chr1:801..1000 Type=UTR

[EST]
glyph   = segments
bgcolor = green
key     = Mapped Expressed Tags

EST	yk260e10.5	Chr3:15569..15724
EST	yk672a12.5	Chr3:537..618,3187..3294
EST	yk595e6.5	Chr3:552..618

[PRED]
glyph       = heat_map
start_color = yellow
end_color   = blue
min_score   = 0
max_score   = 100
citation    = Bluer exons have higher prediction values
key         = Predicted genes

PRED	"Gene 1"	Chr1:518..616 score=50
PRED    "Gene 1"        Chr1:661..735 score=80
PRED    "Gene 1"        Chr1:3187..3365 score=50
PRED	"Gene 2"	Chr1:16626..17396 score=85
PRED    "Gene 2"        Chr1:17451..17597 score=90

The Data Lines

Each annotation occupies one or more lines. It contains three to five columns, delimited by tabs or spaces:

Column 1, the feature type
The first column is the feature type. Any description is valid, but a short word, like "knockout" is better than a long one, like "Transposon-mediated knockout". Later on you can provide a long descriptive name in the formatting key if you desire. If the feature type contains white space, you must surround it by double or single quotes.
Column 2, the feature name
This is the name of the feature. The name will be displayed above the feature when there's room for it and name display is turned on. Shorter names are more attractive than long ones. If the name contains white space, you must surround it by white space. Use empty quotes ("") if there is no name to display.
Column 3, the feature position
The third column contains one or more ranges occupied by the feature. A range has a sequence ID indicating the chromosome, contig or other reference sequence on which the feature resides, plus a start and end position, and is expressed either as "seqID:start..stop" or "seqID:start-stop". Use whichever form you prefer. You can express a feature that occupies a discontinuous set of ranges, such as an mRNA aligned to the genome, by providing a list of ranges separated by commas. Example:
      chr3:1..10,49..80,110..200
      
There should be no spaces before or after the commas. If there are, enclose the entire range in quotes.

To describe an oriented feature that is on the minus strand, such as a transcribed gene, simply reverse the order of the start and stop ranges. For example:

      chr1:200..110,80..49,10..1
      
The strandedness is only displayed when using an arrowhead glyph, such the "transcript" glyph or the generic glyph with the strand_arrow=1 option. See Customizing the display for details.

All ranges uses the coordinate system of the most recently declared reference landmark.

Column 4, Tags [optional]
The fourth column, if present, is treated as a description. The description will be printed at the bottom of the feature. If there is no description, either leave blank, or use empty quotes. If there is whitespace in the description, surround it with quotes. You can also enter attribute=value information here for processing by certain glyphs. The combinations you are likely to use currently are URL=http://some.place to indicate a URL to link to, Note="some note" to provide a descriptive caption to print under the feature, Score=XXXXX (where XXXX is some numeric value) to give the feature a score for those glyphs that chart numeric values, and Type="some type" to create genes and other complex multipart features.

See Customizing the display for details.

If most of your features are on the same chromosome, then you can insert a reference=<seqid> line to indicate the default sequence ID:

reference=Chr1
PRED	"Gene 1"	518..616 score=50
PRED    "Gene 1"        661..735 score=80
PRED    "Gene 1"        3187..3365 score=50
PRED	"Gene 2"	16626..17396 score=85
PRED    "Gene 2"        17451..17597 score=90

Chr1 will now be the default chromosome until the next reference= line is encountered.

In addition to this format, you may use the standard GFF format for your data. Details can be found at the Sanger Centre.

Features and Subparts

To create a feature that has multiple subparts, you can indicate the type of each subpart using the Type="some type" tag. Usually you will use this for coding gene transcripts when you want to distinguish the coding and non-coding portions of the gene.

Here is a simple example:

mRNA B0511.1   Chr1:1..100                     Type=UTR;Note="Putative primase"
mRNA B0511.1   Chr1:101..200,300..400,500..800 Type=CDS
mRNA B0511.1   Chr1:801..1000                  Type=UTR
The top level feature's primary tag will be "mRNA", as indicated in the first column. It will contain five subparts, a 5' UTR spanning positions 1..100, a series of three CDS (coding) regions, and a 3' UTR extending from positions 801..1000.

Additional tags that are placed in the first line of the feature, such as the Note, will be applied to the top level. In this example, the note "Putative primase" will be applied to the mRNA at the top level of the feature:

Grouping

You can group related features together. The layout will attempt to keep grouped features together, and will connect them with a dotted or solid line if the connector option is specified.

A group is created using a line that contains just two columns consisting of the feature type and name. This is followed by a series of data lines in which the feature type is blank. For example:

cDNA-clone  yk53c10
            yk53c10.5       18892-19154
            yk53c10.3       15000-15500,15700-15800

[cDNA-clone]
glyph = segments
connector = dashed

This example creates a group of type "cDNA-clone" named Yk53c10. It consists of two sub-features, one the 5' EST and the other the 3' EST. The two configuration section that follows this group says to use the "segments" glyph and to connect the parts using a dashed line. This is described in more detail later.

You can add URLs and descriptions to the components of a group, but not to the group as a whole.

Comments

You can place a comment in the annotation file by preceding it with a pound sign (#). Everything following the pound sign is ignored:

# this is a comment

Customizing the Display

The browser will generate a reasonable display of your annotations by default. However, you can customize the appearance extensively by including one or more configuration sections in the annotation file. In addition to changing the size, color and shape of the graphical elements, you can attach URLs to them so that the user will be taken to a web page of your choice when he clicks on the feature.

Here is an example configuration section. It can appear at the top of xthe file, at the bottom, or interspersed among data sections:

 # example file
 [general]
 height = 12
 strand_arrow = 1

 [EST]
 glyph = segments
 bgcolor= yellow
 connector = dashed
 height = 5

 [FGENES]
 glyph = gene
 bgcolor = green
 description = 1

The configuration section is divided into a set of sections, each one labeled with a [section title]. The [general] section specifies global options for the entire image. Other sections apply to particular feature types. In the example, the configuration in the [EST] section applies to features labeled as having type "EST", while the configuration in the [FGENES] section applies to features labeled as predictions from the FGENES gene prediction program. Options in more specific sections override those in the general section.

Inside each section is a series of name=value pairs, where the name is the name of an option to set. You can put whitespace around the = sign to make it more readable, or even use a colon (:) instead if you prefer. The following option names are recognized:

OptionValueExample
bgcolor Background color of each element blue
bump Prevent features from colliding (0=no, 1=yes) 1
connector Type of group connector (dashed, hat or solid) dashed
description Whether to print the feature's description (0=no, 1=yes) 0
fgcolor Foreground color of each element yellow
glyph Style of each graphical element (see list below) transcript
height Height of each graphical element (pixels) 10
key Key to the feature. This is a human-readable description that will be printed in the key section of the display ESTs aligned via TwinScan 1.2
label Print the feature's name (0=no, 1=yes) 1
linewidth Width of lines (pixels) 3
link URL to link to. This is a Web link in which certain variables beginning with the "$" will be replaced with feature attributes. Recognized variables are: $name - the name of the feature, and $type - the type of the feature (e.g. EST). link = http://www.your.site/db/get?id=$name;type=$type
citation This is a longer narrative description of the feature intended to identify the author and detailed description of the method. It can be either a text description or a link. http://your.site.org/detailed_description.html
strand_arrow Indicate feature strandedness using an arrow (0=no, 1=yes). NB: Strandedness is depicted differently by different glyphs, and in some cases is the default. 1
section Indicates where in the gbrowse window this type of feature should be placed: "details"=details panel; "overview"=overview panel; "region"=region panel (if there is one for this source); "details+overview"=both panels; "details+overview+region"=all three panels.

"details" is the default.

details+overview

The bump option is the most important option for controlling the look of the image. If set to false (the number 0), then the features are allowed to overlap. If set to true (the number 1), then the features will move vertically to avoid colliding. If not specified, bump is turned on if the number of any given type of sequence feature is greater than 50.

Unlike the data section, you do not need to put quotes around option values that contain white space. In fact, you can continue long option values across multiple lines by putting extra space in front of the continuation lines:

[GenomeAlign]
citation = The pseudoobscura genome was aligned to melanogaster using
   GenomeAlign version 1.0.  High-similarity regions are shown in
   blue, low similarity regions are shown in orange.  The work was
   performed by Joe Postdoc, and is currently in press.

Some glyphs also have glyph-specific options. These are described in detail below.

Colors

Colors are English-language color names or Web-style #RRGGBB colors (see any book on HTML for an explanation). The following colors are recognized:

white coral darkslateblue green lightpink mediumslateblue paleturquoise sienna
black cornflowerblue darkslategray greenyellow lightsalmon mediumspringgreen palevioletred silver
aliceblue cornsilk darkturquoise honeydew lightseagreen mediumturquoise papayawhip skyblue
antiquewhite crimson darkviolet hotpink lightskyblue mediumvioletred peachpuff slateblue
aqua cyan deeppink indianred lightslategray midnightblue peru slategray
aquamarine darkblue deepskyblue indigo lightsteelblue mintcream pink snow
azure darkcyan dimgray ivory lightyellow mistyrose plum springgreen
beige darkgoldenrod dodgerblue khaki lime moccasin powderblue steelblue
bisque darkgray firebrick lavender limegreen navajowhite purple tan
blanchedalmond darkgreen floralwhite lavenderblush linen navy red teal
blue darkkhaki forestgreen lawngreen magenta oldlace rosybrown thistle
blueviolet darkmagenta fuchsia lemonchiffon maroon olive royalblue tomato
brown darkolivegreen gainsboro lightblue mediumaquamarine olivedrab saddlebrown turquoise
burlywood darkorange ghostwhite lightcoral mediumblue orange salmon violet
cadetblue darkorchid gold lightcyan mediumorchid orangered sandybrown wheat
chartreuse darkred goldenrod lightgoldenrodyellow mediumpurple orchid seagreen whitesmoke
chocolate darksalmon gray lightgreen mediumseagreen palegoldenrod seashell yellow
coral darkseagreen green lightgrey mediumslateblue palegreen sienna yellowgreen

Glyphs

The ``glyph'' option controls how the features are rendered. The following glyphs are implemented:

NameDescription
generic A filled rectangle.
ellipse An oval
arrow An arrow; can be unidirectional or bidirectional. It is also capable of displaying a scale with major and minor tickmarks, and can be oriented horizontally or vertically.
segments A set of filled rectangles connected by solid lines. Used for interrupted features, such as gapped alignments and exon groups.
gene The "gene" glyph is suitable for drawing coding genes. The coding regions will be drawn using the specified bgcolor, and the UTRs will be drawn in grey. You can change the color of the UTRs by specifying a "utr_color" option. For the gene glyph to work properly, the top level feature must be of type "mRNA" and the subparts of type "UTR", "five_prime_UTR", "three_prime_UTR", or "CDS". See the top of this document for an example.
transcript Similar to segments, but the connecting line is a "hat" shape, and the direction of transcription is indicated by a small arrow.
transcript2 Similar to transcript, but the direction of transcription is indicated by a terminal segment in the shape of an arrow.
anchored_arrow Similar to arrow, but the arrow is drawn in order to take account of features whose end-point(s) are unknown, rather than to indicate strandedness.
primers Two inward pointing arrows connected by a line. Used for STSs.
triangle A triangle, used to represent point features like SNPs, or deletions and insertions. May be oriented north, south, east or west.
xyplot A histogram, line plot or column chart, used for graphic numeric features such as microarray intensity values. To indicate the value you wish to chart, add a score=XXXX note to the description section:
    Intensity    expt1    15569..15724    score=192
    Intensity    expt1    17451..17597    score=1071
    
See Displaying Intensity Plots & Other Numeric Data for full details.
graded_segments A set of connected segments whose colors change intensity according to a score indicated by a "score=XXX" tag. The low and high scores are indicated by "min_score" and "max_score" options in the configuration stanza, and the basic color is indicated by "bgcolor."
heat_map A set of connected segments whose colors change hue according to a score indicated by a "score=XXX" tag. The low and high scores are indicated by "min_score" and "max_score" options in the configuration stanza, and the start and ending hues are indicated by "start_color" and "end_color." A feature with score equal to min_score will be displayed using start_color, while a feature with score equal to max_score will be displayed using end_color. Intermediate scores are displayed by blending the two hues.
trace Reads a SCF sequence file and displays the trace graph. For this glyph to work, the trace file must be placed on a web-accessible FTP or HTTP server and the location indicated by a "trace" tag:
    Read    ef18222    15569..15724    trace=http://my.host/traces/ef1822.scf
    

The following glyph-specific options are recognized:

GlyphOptionDescription
arrow, anchored_arrow tick Draw major and minor ticks on arrow. (0 = no ticks, 1 = major ticks, 2 = major & minor ticks)
  parallel Whether to draw the arrow parallel to the sequence or perpendicular to it (1=parallel, 0=antiparallel).
  northeast, east Force a north or east arrowhead. (The two option names are synonyms.) (0=false, 1=true)
  southwest, west Force a south or west arrowhead. (The two option names are synonyms.) (0=false, 1=true)
  double force doubleheaded arrow (0=false, 1=true)
  base Draw a vertical base at the non-arrowhead side (0=false, 1=true).
  scale Reset the labels on the arrow to reflect an externally established scale.
gene utr_color Color of the UTRs
  thin_utr If set to a non-zero value, then UTRs will be drawn as thin boxes
  decorate_introns If set to a non-zero value, then introns will be decorated with little arrows indicating the direction of the transcript
primers connect Whether to connect the inward-pointing arrowheads by a line (0=false, 1=true)
  connect_color Color of the connecting line
triangle point Is this a point-like feature? If true, the triantle will be drawn at the center of the range, and not scaled to the feature width. (0=false, 1=true)
  orient Orientation of the triangle. (N=north, S=south, E=east, W=west)
xyplot graph_type Type of graph (histogram, boxes, line, points, linepoints)
  min_score Minimum score for feature (will be level 0 on graph)
  max_score Maximum score for feature (will be level 0 on graph)
  scale Where to draw the Y axis scale, if any (left, right, both, none)
  point_symbol When using points or linepoints graph types, controls the symbol to use for the data points. One of triangle, square, disc, point, or none.
  point_radius The radius of the symbols, if applicable, in pixels
graded_segments min_score Minimum score for the feature (will be drawn as a white segment)
  max_score Maximum score for the feature (will be drawn as a segment with full intensity bgcolor)
heat_map min_score Minimum score for the feature (the segment will be drawn with the starting hue)
  max_score Maximum score for the feature (the segment will be drawn with the ending hue)
  start_color Color for segments with the minimum score
  end_color Color for segments with the maximum score
trace trace Specify the trace path or URL to use for this feature.
  trace_prefix String to prepend to each trace path. You may prepend a directory or a partial URL.
  trace_height The height in pixels that the trace will be drawn.
  vertical_spacing Vertical distance from the box that shows the physical span of the feature to the top of the picture (in pixels).
  glyph_delegate Glyph to use when zoomed out too far for the trace to be drawn.
  a_color Color of the line representing Adenine on the trace.
  c_color Color of the line representing Cytosine on the trace.
  g_color Color of the line representing Guanine on the trace.
  t_color Color of the line representing Thymine on the trace.
  show_border Show the black border from around the trace (0=false, 1=true)

Displaying Intensity Plots & Other Numeric Data

You can upload microarray intensity data sets and other numeric data. The plot of the data will be displayed as a histogram or line chart superimposed on the genomic annotations.

Here is a simple template for you to follow. The result is shown on the right.

[expression]
glyph = xyplot
graph_type=boxes
fgcolor = black
bgcolor = red
height=100
min_score=0
max_score=110
label=1
key=Expression Level


reference=B0019
expression       liver   10000..12000    score=10
expression       liver   12001..19999    score=50
expression       liver   20000..25000    score=100

expression       kidney   10000..12000    score=80
expression       kidney   12001..19999    score=10
expression       kidney   20000..25000    score=100

The [expression] section says to use the xyplot type of glyph, to set its type to "boxes" (a column chart), to make the fore and background colors black and red respectively, to set the height of the chart to 100, and to set the minimum and maximum values for the Y axis to 0 and 110 respectively. We also add a label and a human-readable track key.

The data section defines two experiments to show in the track. Both experiments use probes whose positions are relative to landmark B0019 (you can of course use chromosome coordinates, or whatever you choose). Both experiments are of type "expression", but one is the "liver" experiment and the other is the "kidney" experiment, as indicated in the second column. The third column contains the coordinates of each assay point, and the fourth column contains the score=XXX attribute, where XXX is the intensity value.

See the chart in the previous section for the xyplot glyph options.


Publishing Annotations

If you have access to a web server, you can easily publish your annotations. Simply take the annotation data file and place it on a Web server that is accessible to the Internet (or at least to the server on which the Genome Browser runs).

Type the URL of your annotation file into the Enter Remote Annotation URL text field of the genome browser screen. Your annotation file be will accessed by the web server on which the genome browser runs, loaded and displayed. Repeat this process to add more external annotation tracks to the display. To remove a URL, just delete the contents of the field.

Right-click on the bookmark this link link in order to save the information to a URL that you can bookmark or mail to your colleagues.


BUGS IN THIS SOFTWARE

Please report them to the author.


AUTHOR

Lincoln Stein <lstein@cshl.org>


2008.The servers are free for academic use. Please contact IPR Cell for commercial use. All third party trademarks are owned by their respective owners and used with permission

FishMap development has been generously funded by the Council for Scientific and Industrial Research (CSIR), India (Grant No FAC002)

FishMap is hosted and maintained at the G N Ramachandran Knowledge Center for Genome Informatics at the Institute of Genomics and Integrative Biology

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