Browser Requirements

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User Interface

  1. Genome and data selection: Copy/paste the input file containing gene/genomic region identifiers and select the appropriate file type. Alternatively, use the identifier search ("Identifier")- or BLAST- buttons to search for relevant gene identifiers. Click "Visualize context".
  2. On display: This box keeps track of the data added to your circular map. You can remove a data-track by clicking the corresponding "delete" link.
  3. Data import: This box allows users to upload genomic elements (e.g. regulatory motifs, promoters), numerical gene-data (e.g. RNA-seq-, microarray data) and custom color schemes. Select the file-type, set a name and upload a file in the appropriate format. Subsequently, the corresponding data will be available in the Feature selection in the input-box.
  4. Elements and genomic context: For each imported set of genomic elements plots visualizing different characteristics with respect to their genomic context are available in this box.
  5. Circular genome map: The actual circular genome map. The map will be updated each time you add a ring to it.
  6. Map conversion: Click one of these three buttons to save the current map in SVG-, PNG- or PDF- format
  7. Legend: Click this link to generate a custom legend for your circular map.

Genome and data selection

The data input-box defines what will be visualized in the circular genome map. This box works stepwise; in each step you add a new ring (i.e. datatrack) to the circular genome map.

  1. Set your organism of interest and corresponding genome of interest.
  2. Select the type of data (feature) to include.
  3. Set the coloring.
  4. Set the location of the ring within the circular map.
  5. Click "Add Ring" to add your data-track.

1. Genomes

Type (a part of) the name of the organism of interest. Matching organism names will be displayed, click on your organism of interest to select. Next, the select your genome of interest (e.g. chromosome or possibly plasmid) that are available in the genome select. A table with all available organisms and their corresponding genomes is avaiable here.

2. Data

Select using the dropdown-box which data you want to visualize. An overview of the available types of data is given in table 1.


Table 1 - Overview of data-domains available in circular genome maps
Data-domain Available coloring Source
Sequence properties
Genes on plus strand User selection / COG category / Subcellular location Internal database (RefSeq)
Gene - strand User selection / COG category / Subcellular location Internal database (RefSeq)
GC percentage User selection (spikes) / Color gradient Internal database
GC skew User selection (spikes) / Color gradient Internal database
AT skew User selection (spikes) / Color gradient Internal database
Additional features
Background shading User selection NA
Coordinates User selection NA
Genome Information (title) User selection NA
Matching keywords User selection Internal database
User upload
Sequence elements User selection File upload (format)
Quantative gene-data User selection (spikes) / Color gradient File upload (format)
Pre-defined coloring Variable File upload (format)

3. Color scheme

The color-scheme used to represent the data select in the previous step. A selection can be made on basic colors, or on any color can be set using the color picker. When quantative data (e.g. GC%, GC-skew, uploaded quantative gene-data) is selected in the previous step, the option Red-Yellow-Green becomes available as well. When the latter option is selected, quantative data will be represented using a color gradient instead of (bargraph like-) spikes.

4. Position Ring

Position and width of the ring, defined by the outer-radius and inner-radius, for which 100% is the most outer part of the map and 0% is the center of the map.

Data features

Matching keywords

This can be used to highlight a specific set of genes that match your search. You can search genes based on:

In case of COG-codes, CiVi will only recognize the code ("COG"+ four numbers), not the description. For COG categories, use the one letter abbreviation and not the name. Please consult the supplied links for the COG-codes and COG category abbreviations.

Background shading

This feature simply adds a ring in the selected color which subsequently can be used as a background to increase color contrast with other data. Additonally, it can make the map visually more attractive when correctly used. In order to use it as a background, first add this before you add the data and set a identical position for the background shading and the other feature.

Genome Information (title)

This feature can be used to enter a text that will be included in the center of your circular map. A common usage is to set the species name in here (CiVi will automatically fill in the name of the selected species).

On Display

The "On Display"-box keeps tracks of the individual rings that have been added to the circular genome map. When a ring is added it's position and type of data is listed here. To delete a ring click the "delete" link on the right side of the box.








Data Import

Include your own data by uploading data in this box. This data can then be used to include in the comparative genome maps but can also be used to create a comparative genome map on.

First select the type of data you want to upload: genomic elements (e.g. regulatory elements, promoters or any genomic element) or gene-scores (e.g. microarray data, identity scores or any numerical score assigned to a gene). Then select the with a appropriate format file on your computer and click "Upload". Now, the checkbox of the uploaded type of data becomes available. Check the checkbox to include the data in a comparative genome map.
Or click on the blue arrows (score ascending / descending) to view a comparative context map based on the uploaded data.

Genomic elements

The input for genomic elements is a tab separated file with the following data on each line: a genome ID (NC code), a start position in nt., a stop position in nt., the strand*, a numerical score* and a color* (defined by a hex code or basic color name).

* = optional, leave blank when not available

Format

NC_accession Start Stop Strand* Score* Color*
.. .. .. .. .. ..
.. .. .. .. .. ..

Example

NC_000913 5640 5669 + 0.9630 Blue
NC_000913 25766 25795 + 0.9815 Blue
NC_000913 39151 39180 - 0.9444 Red
NC_000913 72191 72220 + 0.9259 Blue
NC_000913 111550 111579 + 0.9259 Blue
NC_000913 138767 138796 + 0.9630 Blue
NC_000913 173559 173588 + 0.9259 Blue
NC_000913 216059 216088 + 0.9815 Blue

Example file: putative sigma54 binding sites in L. plantarum WCFS1 (NC_004567)

Quantative gene-data

The input for quantitative gene-data (i.e. microarray or RNA-seq data) is a tab separated file with the following data on each line: a gene identifier (NCBI GI-code or NCBI locus tag) and a score or ratio. A red-to-green (low-to-high) will be determined based on the input scores.

Format

NCBI-gi Score or ratio
.. ..
.. ..

Example

116333625 1.5
116333626 -0.6
116333627 1.2
116333628 -1

Example file: microarray data of L. plantarum WCFS1 (NC_004567) sigma-54 mutant.

Custom coloring

The input for custom coloring is a tab seperated file with the following data on each line: : the start position, the stop position, the outer radius (0-100), the inner radius (0-100, must be smaller then the outer radius) and a color (defined by a hex code or html color name).

Format

Start position Stop position Outer radius (0-100) Inner radius (0-100) Color
.. .. .. .. ..
.. .. .. .. ..

Example

20439 40398 100 80 #D0D0D0
60000 700000 100 80 green
69000 700000 80 70 red

Example file: custom coloring scheme


Genomic Elemenent analysis

This box provides additional plots for uploaded sequence elements. These plots will be automatically generated when a data-set is uploaded ("Data import"-box). In the case multiple sets have been uploaded the user can select the set of interest using the dataset selection. All (annotation-) data on the local genomic context of elements can be retrieved using the "Generate context table" link.

The first boxplot summarizes the orientation of the gene-pairs neighbouring the elements. The type of genepair orientation (intragenic, co-oriented, divergent or convergent) can indicate functionality (promotor, terminator, etc.) and assists curation of prediction accuracy (e.g. too many intragenic hits).

Click "View/hide distance plots" to show distributions of the distance of the elements to the upstream and downstream genes. Depending on the orientation of the gene-context the most informative distances are visualized:

Intragenic Co-oriented Divergent Convergent

An example of the plots generated for co-oriented elements is shown on the right side. The icons in the header represent the genes (arrows) and element (circle) and the analyzed distance (indicated in red).


Example Circular Genome maps


Stepwise, the following rings were added:

Ring Species Data feature Coloring Outer radius Inner radius
Ring 1 Bacillus subtilis str. 168 Genes plus-strand COG category 100 96
Ring 2 Bacillus subtilis str. 168 Genes minus-strand COG category 95 91
Ring 3 Bacillus amyloliquefaciens str. 168 Genes plus-strand COG category 87 83
Ring 4 Bacillus amyloliquefaciens str. 168 Genes minus-strand COG category 82 78
Ring 5 NA Background shading Pick color: #ebebeb 74 52
Ring 6 Bacillus subtilis str. 168 GC-skew purple 74 53
Ring 7 Bacillus subtilis str. 168 Sequence Elements: Cre-sites high affinity (upload input file) Specified in input 53 49
Ring 8 Bacillus subtilis str. 168 Quantative data: CcpA low induction (upload input file) red-yellow-green gradient 49 45
Ring 9 Bacillus subtilis str. 168 Sequence Elements: Cre-sites low affinity (upload input file) Specified in input 45 41
Ring 10 Bacillus subtilis str. 168 Quantative data: CcpA high induction (upload inputfile) red-yellow-green gradient 41 37
Ring 11 Bacillus subtilis str. 168 Matching keywords :: COG Category :: "G" (carbohydrate transport and metabolism) Blue 33 29