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The data input-box defines what will be visualized. Users should select the type of input ("Input type"-dropdown) and paste their identifiers in the Input data field. The following data can be used as input (click for details on the format)
In case the user does not have the a list of gene identifiers, genes and corresponding identifiers can be obtained via the built-in gene-search (click button "Identifier"). Alternatively, users can perform a BLAST search (click button: "BLAST").
To use the identifier search: type the name of the species of interest and click on it when it appears in the form (the form will autocomplete your entry based on available species). Next, select the type of search term you want to search on. Now enter your search term and select your gene of interest to append it to your selected genes. Finally, click "Load as input" and close the window.
To use BLAST: supply the amino acid sequence of your protein of interest. Set the number of maximum hits you want to retrieve, select the organisms in which you want to search in (limited at maximal 50) and click "Blast". When the Blast search is finished, a window with results will be displayed. You can now load all resulting NCBI GI-codes in MGcV using the "Load complete list"-button. You can also make a subselection by selecting your hits of interest with the plus-icon. Then click "Load subselection" and close the Blast window.
Use this box to make changes in the appearance of the output map. Click the "Adjust settings" button to apply changes that were made.
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 gene scores (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|
Example file: putative sigma54 binding sites in L. plantarum WCFS1
Example file: microarray data of L. plantarum WCFS1 sigma-54 mutant.
The input for custom coloring of genes is a tab seperated file with the following data on each line: : a gene identifier (NCBI GI-code or NCBI locus tag) and a color name or code. The color column can be assigned using a code code or html color name. Click here for html color names and hex codes.
|NCBI-gi||color name or code|
Example file: custom coloring scheme L. plantarum WCFS1
You can select genes of interest simple by clicking on them. The border of selected genes will color red and appear then in this box. To retrieve functional/sequence data for these genes, select the data type of interest and click "Export data". To reset the set of genes of interest click "Clear selection". Available data types: