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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.
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.
Select using the dropdown-box which data you want to visualize. An overview of the available types of data is given in table 1.
|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|
|Background shading||User selection||NA|
|Genome Information (title)||User selection||NA|
|Matching keywords||User selection||Internal database|
|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)|
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.
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.
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.
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.
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).
The "On Display"-box keeps tracks of the individual rings that have been added to the
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.
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.
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
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.
|NCBI-gi||Score or ratio|
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).
|Start position||Stop position||Outer radius (0-100)||Inner radius (0-100)||Color|
Example file: custom coloring scheme
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:
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).
|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|