Browser Requirements

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User Interface

  1. Input: 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. Map settings: Use this box to alter the appearance of the comparative context map. Click the "Adjust settings" button to apply changes.
  3. Data import: This box allows users to upload genomic elements (e.g. regulatory motifs, promoters). Select the file-type and upload a file in the appropriate format. Subsequently, the corresponding checkbox can be checked to include this data in the genome map..
  4. Data export: Retrieve data for selected genes (e.g. upstream regions, gene sequences, cog categories). Click on a gene to include, click again to exclude. Select the data type you want to retrieve and click "Export data". Click "Clear selection" to remove all selected genes
  5. Comparative genome map: The actual genome map. The maps are interactive: hover genes for additional information (e.g. NCBI gi, gene product, COG, coordinates) and click genes to add them to the data export set.
  6. Map conversion: Click one of these two buttons to save the current map in either PNG or PDF format
  7. Practical links: Links to the documentation, legend, MEME etc.

Data input

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.

NCBI-gi

Format

NCBI-GI
NCBI-GI
..
..

Example

Input:
28378694
116333628
116492506
116513149
116617828
125625241
Output:
Example output

Locus tags

Format

locus tag
locus tag
..
..

Example

Input:
b1515
b4086
b2148
ECDH10B_1646
ECDH10B_4277
ECDH10B_2305
Output:
Example output

Newick trees

Format

Newick tree format (more information on wikipedia). The leaf labels must contain a NCBI-GI code. For example, you can use the fasta headers as supplied by the FTP server of Refseq (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/).

Example

Input:
( gi|116492506_PEPE_0738_Pediococcus_pentosaceus__ATCC_25745:0.18695, ( gi|16803338_lmo1298_Listeria_monocytogenes__EGD-e:0.18875, ( ( ( gi|212639339_Aflv_1508_Anoxybacillus_flavithermus__WK1:0.12356, gi|138894845_GTNG_1181_Geobacillus_thermodenitrificans__NG80-2:0.14012) :0.04233, ( gi|16078808_BSU17450_Bacillus_subtilis_subtilis_168:0.08345, gi|154686158_RBAM_017250_Bacillus_amyloliquefaciens__FZB42:0.07705) :0.10945) :0.01302, gi|172057119_Exig_1082_Exiguobacterium_sibiricum__255-15:0.23419) :0.05650) :0.00540, ( ( ( ( gi|116513149_LACR_2513_Lactococcus_lactis_cremoris_SK11:0.00245, gi|125625241_llmg_2485_Lactococcus_lactis__cremoris_MG1363:0.00301) :0.20345, gi|116617828_LEUM_0716_Leuconostoc_mesenteroides_mesenteroides_ATCC_8293:0.22239) :0.03079, gi|116333628_LVIS_0991_Lactobacillus_brevis__ATCC_367:0.18359) :0.01012, gi|19746805_spyM18_1943_Streptococcus_pyogenes__MGAS8232:0.19447) :0.00702);
Output:
Example output

Genomic positions

Format

NC_code, Start position, Stop position
NC_code, Start position, Stop position
.., .., ..
.., .., ..

Example

NC_000913, 14000, 15300
NC_010473, 14000, 15300
NC_017631, 12200, 13500
NC_009800, 12100, 12400

Output:
Example output

Map Settings

Use this box to make changes in the appearance of the output map. Click the "Adjust settings" button to apply changes that were made.

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

Gene-scores

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.

Format

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

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

Example

116333625 1.5
116333626 -0.6
116333627 1.2
116333628 -1

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

Custom coloring

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.

Format

NCBI-gi color name or code
.. ..
.. ..

Example

116333625 CornflowerBlue
116333626 -0.6
116333627 IndianRed
#F0E68C #CD5C5C

Example file: custom coloring scheme L. plantarum WCFS1


Data Export

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: