fancyGENE Help
fancyGENE is a fast and user-friendly tool for drawing pictures of gene structures, correctly mapping each object on the corresponding genomic locus.
All the most important features, like exons, introns, markers and domains can be easily visualized, for one or more genes or for several isoforms at the same time.
Input data can include a single mrna or isoform as well as lists of genes.
Output files can be in PNG or PDF format.
Each element of a PDF file can then be indipendently edited using you favourite vector graphics editor.
Schema of the FancyGENE webserver:
- Upload or paste gene coordinates in one of the input formats
- FancyGENE load your data and scale the genomic coordinates according to the choose output
- The scaled data are then drawed on the selected surface
- The user are redirected to the resulting page, where he can dynamically change the appereance of single objects and can download the output file
For an introduction to fancyGENE look at the tutorial.
Here we provide a systematic description of all avaliable graphic options and formats.
- Simple
The simple format is used to describe a single gene/locus:
START(int) END(int) [ STRAND (+|-) ]
The strand (optional) can be + or -.
Additional tags
label: with the tag label, I can specify the gene label. Es:
label my_mRNA 1050 2050 - 3200 4000 - 5100 6000 - 8000 8450 - 10050 11230 -
- Advanced
The advanced format is the main format of FancyGENE (every input is initially converted to this format and then drawed)
The Advanced format:
label(locus|gene_label) tag(intron|exon|utr|marker|domain) start(int) end(int) strand(+|-) or marker_label
Example:
locus locus 7516909 7521006 - NM_001126114 intron 7517383 7517577 - NM_001126114 intron 7517652 7517743 - NM_001126114 intron 7517881 7518223 - NM_001126114 intron 7518334 7518901 - NM_001126114 intron 7519015 7519095 - NM_001126114 intron 7519280 7520036 - NM_001126114 intron 7520316 7520424 - NM_001126114 intron 7520447 7520563 - NM_001126114 domain 5 29 TAD NM_001126114 domain 63 89 LowComp NM_001126114 domain 95 289 P53 NM_001126114 utr 7517250 7517349 - NM_001126114 utr 7520638 7520665 - NM_001126114 exon 7517350 7517382 - NM_001126114 exon 7517578 7517651 - NM_001126114 exon 7517744 7517880 - NM_001126114 exon 7518224 7518333 - NM_001126114 exon 7518902 7519014 - NM_001126114 exon 7519096 7519279 - NM_001126114 exon 7520037 7520315 - NM_001126114 exon 7520425 7520446 - NM_001126114 exon 7520564 7520637 - NM_001126114 marker 7517600 7517601 MarkerA NM_001126114 marker 7517380 7517382 MarkerB
Available TAGS- Tags where the last element is the strand
- exon
- intron
- utr
- Tags where the last element is a label
- marker
- domain
- Tags where the last element is the strand
- GFF and GTF
A description of the General Feature Format (GFF) can be found at the Sanger website
A description of the Gene Transfer Format (GTF) cab be found at the UCSC website
PDF: portble document format, this format presevre the editing capability on the resulting image, that can be opened with your favorite vector graphics software
PNG: portable network graphics format, doesn't preserve editing capabilitites- OUTPUT OPTIONS
Used to define the size of the output images, can be a general format (A4 portait or landscape, 800x600, etc..) or User Defined (the user can specify the dimension of the output image)
INPUT interface options
- used to select the input type
- used to select the output type
- here the user can paste data in every available format
- is also possible to upload data from files
- the gene wizard allow to retrieve coordinates directly from the UCSC database (see tutorial), the user must select the correct UCSC database using the drop-down list. In this version of FancyGENE search the provided identifiers in the regGene table
now is possible to save your configuration (colors, lines, etc...) into an XML file, save it to your desktop and upload it here to restore your configuration- in this section there are buttons used to send data (DRAW), clear the input text box (CLEAR INPUT), reset all graphical parameters (RESET)
Additional Option
- , with this options we can manually specify a locus offset (start and end in basepairs). This feature can be used in the first form to define a locus offset, or in the secondary changes to the resulting image, in order to "zoom" the image at a specific genomic offset
- define the size in Pixel/Points for the the Gene Track
- define the empty space above and below the Gene Track
- , you can specify in which order the genes will be drawed available options are:
- : objects are drawed according to the genomic position
- : objects are drawed according to the order of insertion (in input)
- : objects are drawed in alphabetical order
- and are used to draw/not draw gene label, available label types:
- over the gene
- under the gene
- at the side of the gene
- inside the gene (centered)
- and are used to draw/not draw the strand of the gene, available strand types:
- : an arrow under the gene label represent the strand direction
- : the last exon/utr of the gene show the strand direction
- : the user can provide only exons and utrs, introns are automatically drawed between exons, with this radio button is possible to hide introns.
Appereance
- : specify which type of color will be used: a solid color, a gradient (from a given color to white), no colors
- : specify if the background will be transparent or filled with a specific color
In general, for each object in the image, is possible to change 3 parameters: shape, stroke and color
- SHAPE: in this version of FancyGENE only the INTRON object have different shapes: hat and line
- STROKE: Change the size of the stroke line
- COLOR: change the fill color (color format: RGB). If the color mode is , This RGB color will be used as the main color of the gradient (the other color used for the gradient is always white).
-
- control the appereance of exons
- control the appereance of utrs
- control the appereance of introns
- control the appereance of domains, once the user have added domains to the pictures, this section will dynamically update. Is so possible to specify colors and appereance of single domains in the figure
Add Features
ONCE the we have generated the first image, with the fieldset is possible to interactively add and modify objects.
This is especially useful when the user wants to add domains to an existing object. See the tutorial for an example.
The button can be used to clear the update objects textarea, the button reset all parameters in the interface.
The button NEWLINE and DOMAINS near the gene name allow the user to automatically generate a scaffold that can be used to add objects to the corresponding gene.
