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Load and Submit Sample Data
Example 1: Coronin genes, 28 genes from 12 species.
Example 2: Tubulin genes, 50 genes from 4 species.
Click on link to load and submit example.
Data Upload
Multiple Sequence Alignment
Enter FASTA sequences
Enter multiple protein sequence alignment in the text input field. The alignment must be FASTA-formatted. Protein sequences are matched with the gene structures on the basis of the FASTA header and file names, respectively. For this reason, FASTA headers must not contain any blanks or special characters.
No file uploaded
Upload a multiple protein sequence alignment from your local disk. The alignment must be FASTA-formatted. Protein sequences are matched with the gene structures on the basis of the FASTA header and file names, respectively. For this reason, FASTA headers must not contain any blanks or special characters.
Gene Structures
In order to start GenePainter, GenePainter needs a multiple protein sequence alignment and gene structures. You can upload gene structures generated by WebScipio (recommended) or provide a mapping between species and genes and select the gene structure generation.
No files uploaded
Gene structures must correspond to an alignment sequence. They must be either in YAML format and generated by WebScipio or in GFF v.3 format. File names must equal the corresponding gene name (FASTA header). If the gene structure is in YAML format and specifies a gene name in the YAML description, this gene name must also equal the file name.
Or generate gene structures for selected sequences (Data Center)
Species Mapping (optional)
In order to plot intron gain and loss events onto the phylogenetic tree (based on NCBI taxonomy), GenePainter requires a mapping between gene names (FASTA headers) and species names.
Enter species and select corresponding genes
Enter species name or select it from the autocompletion dropdown and select the corresponding gene name(s) from the list next to the input field. Click 'Save' to save the mapping between current species and selected genes. You can then proceed with the next species.
You can make changes to the species mapping in the 'Unlink genes from species' menu on the right.
No file uploaded
Upload a file containing the mapping of gene names (FASTA headers) and species names from your local disk. Follow the link for more information on the required file format.
PDB File (optional)
In order to map intron positions and phases onto a protein structure, GenePainter requires a PDB file. GenePainter provides scripts for execution in PyMol.
No file uploaded
Upload a PDB file from your local disk. Standard parameters for PDB output are applied, i.e. introns occuring in at least 80% of all genes will be mapped onto chain A. Basis for the mapping is an alignment between first sequence in the multiple sequence alignment and the PDB sequence. For full parameter options, please consider using the stand-alone version of GenePainter.
