Welcome to the Syntenic Density Browser where you can investigate novel syntenic blocks at different ancestral nodes, identified from 49 metazoan species from 18 phyla. You can click on Search Our Database tab above to access the complete dictionary of our dataset, which can be used to search for multiple terms such as genes, gene annotation or species using spaces in between each. Following a search with an interesting result, please note down the last two columns, and first select the Taxonomic Group by clicking on the next tab Choose Taxonomic Group above, and then on the new window that opens, using the dropdown box, please select the multi species block using the BlockID from the search result.

For each multi species block, there are 4 panels presented, all of which are user-interactive. When a taxonomic group is selected, by default all the blocks in that group are summarized in the first two panels, while the third and the fourth panels will be blank. To see a multi species block, you can click on the arrow next to All Blocks and select it by scrolling down, or you can delete using backspace and then type in the block number. Making a selection will only show the results for that block.

First Panel on the top presents the boxplots of the distance distributions for each taxonomic node. When hovered over an individual boxplot, minimum, maximum and interquartile distance values can be seen. Outlier values also appear when hovered over individual points. To focus on any part of interest, click, drag, and select an area. The ability to zoom in on the boxplots this way becomes especially useful in cases where outliers lead to a small view. Double clicking on the plot will return the complete view. From the icons that appear when hovered on just above the right-top of the plot, one can also click on Autoscale to get back to the complete plot. It is also possible to perform some other actions, and even to download the plots using the other available icons. To remove a taxonomic node from the plot, click on its name on the legend on the right. To remove all other nodes and to keep only one node, double click on a node name; which then can be then compared against other nodes by clicking on their names in the legend. Removing a node can also be another way to get a closer view on the rest of the nodes if followed by clicking on Rescale icon, when one of the nodes has an extreme outlier. To bring all nodes back to the plot, double click on a node name in the legend two times.

Second Panel presents the geometric densities of distance distributons. When hovered over, the name of the taxonomic node and the density and the distance values can be seen for each spot of the top of the curves. It is also possible to interact with them as well in the same ways as described for the first panel above.

Third Panel illustrates the orthogroups and the distances between them. You can click and drag the background to move the whole space, or also click on orthogroups and drag them around, or zoom in and out using mouse wheel or the buttons on right bottom to make it easier to see the orthogroup names or the distance values. The legend on the right can also be zoomed in and out. Due to the way the network plot algorithm works, sometimes the distances aren't represented well visually, but the values that can be seen on the links are actual distance values. The orthogroups have 3-letter suffixes that represent the first 3 letters of the taxonomic nodes they belong to, and in randomized cases also an additional R letter.

Fourth Panel is the multi species block dictionary where you can see which species from which taxonomic group contributes to which orthogroup with which genes, together with their scaffolds (or in available cases chromosomes), accession IDs (which have 5 letter species code prefixes followed by an underline), species block IDs, and functional annotations when available. BlockID stands for the Multi Species Block ID. Use the search box on top right to search for terms of interest. More than one keyword can be searched for using spaces in between.

Distance values used in this application are genomic base pair distances corrected by the genome assembly sizes of each species. For blocks with too many orthogroups, please wait until all 4 panels are loaded.

Syntenic Density Browser was built and designed by Fatih Sarigol using the dataset generated by Nicolas Robert under the supervision of Oleg Simakov at the University of Vienna, with contributions from Axel Meyer, Christian Voolstra and Bob Zimmermann. If it is useful for your research, please cite our BMC Genomics publication: Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. Thank you!

Bilateria Novel

Lophotrochozoa Novel

Metazoa Novel

Parahoxozoa Novel

Planulozoa Novel

Vertebrata Novel