Website Quick Guide
- Overview
- Sequence
- Protein
- Browse
- Statistics
The overview section contains a table of all the cultivars used in this project, together with the kind donators of the
cultivars and the donator's contact details. The "Jump to" drop-down list can be used to instantly navigate to a graphical
overview of a particular chromosome in the selected cultivar. Alternative, the cultivar's name (on the left-hand side of the
table) can be clicked to navigate to the cultivar overview page.
Cultivar Overview
The cultivar overview is a schematic overview of the approximate locations of genes on the chromosomes. The chromosomes are
scaled relative to each other, with chromosomes 1 and 11 being the largest and smallest, respectively. This overview gives an
instant impression about where the genes are located and where clusters of genes exist. The relative gene positions are linked
to the actual gene identifiers (as given by Jupe et al, 2013), next to which a graphical representation of the genes
is given.
The genes are represented by rounded boxes, in which the detected NBS domain is colored light-green. The location of the detected
single nucleotide polymorphisms (SNPs) within the NBS domains are indicated dark-green vertical lines. Additional information
about the genes can be requested by clicking on any of the genes. A pop-up window will appear supplying more in detail information,
like the exact genomic location of the SNP and the (downloadable) sequence of the NBS domain. This pop-up box can also be used to
navigate to either the sequence alignment of this particular gene for all cultivars ("view sequence"), or the sequence to protein
translation of this gene ("view protein").
By clicking on the "view sequence"-link presented in the gene information pop-ups, you are redirected to the sequence alignment
page. This page displays all available NBS domain sequences of the selected gene in a multiple sequence alignment fashion. Bases
are colored according to the fields standards and the SNPs are clearly visible due to the red font-color.
The sequence given for each cultivar represents the sequence obtained from Illumina sequencing, where a dash ("-") indicates that
there was no coverage at that particular position. Additional information about the SNP can be requested by clicking on them. An
additional pop-up will appear displaying the exact genomic location, and the reference and alternative allele(s) and their coverage.
Additionally, you can request the gene information by clicking on any of the cultivar names and a similar pop-up as the one given
on the cultivar overview page will be displayed.
This page furthermore contains options for setting the visibility of desired cultivars and bulk-download off all sequences
displayed on page (accessible by clicking on the "Alignment" box, containing the gear image, at the top of the page). The selection
or deselection of cultivars can be particularly helpful if one is only interested in comparing a small(er) number of cultivars. This
selection can furthermore be saved for later use (for this function Cookies must be turned on in the browser). This allows for quick
analysis of multiple genes, without the need of selecting/deselecting the desired cultivars with each new gene comparison.
By clicking on the "view protein"-link presented in the gene information pop-ups, you are redirected to the translated nucleotide
sequence. The NBS domain sequence is translated in all six reading frames and the SNPs and codon's containing SNPs are marked in red.
The amino acids displayed in red, are the amino acid as they are present in the reference genome (DM v4.03). By clicking on any of them,
a small pop-up will appear, containing the reference codon and the encoded amino acid, and the alternative codon(s) and their respective
amino acids.
The search and browse page allows for the quick selection of the desired gene. User's can either use the search field or select the
desired cultivar. The search field allows for searching based on the gene names/identifiers or based on a genomic region. Another
possibility is to select a cultivar and than select the desired gene. Both methods will result in list of genes that fulfil the
search/selection criteria. By clicking on one of the genes, the detailed information can be viewed, similar to the cultivar overview page.
The statistics page quickly lists some basic statistics of the SolariX project, such as the number of cultivars, R-genes and detected SNPs.
It furthermore contains a list of statistics for each cultivar. For each cultivar the number of R-genes in which at least one
SNP was detected is listed, together with the total number of SNPs found in this cultivar and the average number of SNPs per gene. The
name of the cultivar furthermore links directly to the cultivar overview page.