At the top of each page in IVCDB, there is a navigation bar. Users can click on the corresponding options in the navigation bar to go to the subpages they are interested in.

The homepage of IVCDB contains a navigation card bar. The card bar displays the contents of different parts of IVCDB, including the quantity of data or content and a brief classification summary. Similar card bars also exist in other subpages of IVCDB.

On the navigation page for virus distribution visualization, users can enter different virus distribution visualization pages by clicking on different card bars, which are distinguished based on geographical location and viral taxonomic level.

The virus distribution visualization includes the map window on the left and the sidebar on the right. The virus isolates are displayed as dots in the map window, and users can drag and zoom in/out the map as needed. At the top of the sidebar, users can filter the virus isolates displayed in the map window through the filter bar. The content that can be filtered includes the subfamily and genus of the virus isolates, and the continent where the virus isolates were isolated. The middle part of the sidebar shows the number of virus isolates displayed in the map window under the current selection conditions in real time. The legend is displayed at the bottom of the sidebar.

Users can view the summary information of each virus isolate by clicking on the dots representing the virus isolates in the map window. Users can also go to the detail page of the virus isolate through the link in the bottom of the summary information window. The summary information contains the following contents:

On the navigation page for dataset and navigation page for virus genome, users can enter different dataset of virus isolates pages by clicking on different card bars, which are distinguished based on viral taxonomic level.

The dataset and virus genome are both presented in the form of tables. Users can enter the content they want to retrieve in the search bar. The columns with sort buttons in the table header can be arranged in ascending or descending order by clicking. The toolbar includes functional buttons for full-screen display, selective display of certain columns, and reset of the table.

By clicking on the genome link, users can go to the corresponding external database. By clicking on the taxonomic level link, users can view the dataset/genome of this taxonomic level within the virus dataset/genome. By clicking on the detail link, users can go to the detailed page of the virus isolate.

The tables contain the following contents:

Users can enter the detail page of each virus isolate through the links in virus distribution visualization, dataset, virus genome, and the interactive evolutionary tree in evolutionary tree.

The detail page of the virus isolate mainly consists of the following seven parts: summary information, related picture, genomic information, genome browser, reannotated ORF/protein, original ORF/protein, and download link.

The summary information contain the following contents:

The related picture shows pictures related to the virus isolate, such as electron microscope images of virus particles, infected animals, infected tissue sections or cell images, etc. A brief note, the source, and copyright information are attached below the picture.

The genomic information contain the following contents:

The genome browser shows the results of the reannotation and the original annotations. The red and orange in the upper part of the genome browser represent the reannotated ORFs, and the green and blue in the lower part represent the original ORFs (if present). Among them, red and green represent the forward ORFs, while orange and blue represent the reverse ORFs.

The reannotated ORF/protein and original ORF/protein present the ORFs/proteins from the standardized genome annotation pipeline and the ORFs/proteins from Genbank databases in the form of tables, respectively. The tables contain the following contents:

The nonredundant proteins database is presented in the form of tables. Users can enter the content they want to retrieve in the search bar. The columns with sort buttons in the table header can be arranged in ascending or descending order by clicking. The toolbar includes functional buttons for full-screen display, selective display of certain columns, and reset of the table.

By clicking on the feature link, users can enter the corresponding homologous superfamily, family, domain, unintegrated family/domain, enzyme, orthology, or pathway detail page in InterPro or KEGG. By clicking the download link, users can download the amino acid sequence file or the structure file of a certain core gene separately. Users can also select core genes simultaneously on the far left of the table and then download the amino acid sequence files and the structure files in batches through the "Download fasta file" and "Download structure file" button in the toolbar. By clicking on the detail link, users can go to the detailed page of the core gene.

The tables contain the following contents:

On the navigation page for core genes, users can enter different core genes pages by clicking on different card bars, which are distinguished based on viral taxonomic level.

The core genes are presented in the form of tables. Users can enter the content they want to retrieve in the search bar. The columns with sort buttons in the table header can be arranged in ascending or descending order by clicking. The toolbar includes functional buttons for full-screen display, selective display of certain columns, and reset of the table.

By clicking on the feature link, users can enter the corresponding homologous superfamily, family, domain, unintegrated family/domain, enzyme, orthology, or pathway detail page in InterPro or KEGG. By clicking the download link, users can download the amino acid sequence file or the structure file of a certain core gene separately. Users can also select core genes simultaneously on the far left of the table and then download the amino acid sequence files and the structure files in batches through the "Download fasta file" and "Download structure file" button in the toolbar. By clicking on the detail link, users can go to the detailed page of the core gene.

The tables contain the following contents:

Users can enter the detail page of each nonredundant protein and core gene through the detail links in nonredundant proteins database, core genes, and the reannotated ORF/protein and original ORF/protein parts in the detail page of virus isolate.

The detail page of protein consists of the following five parts: summary information, protein structure, protein annotation, location of proteins in the genome, and protein sequence.

The summary information contain the following contents:

The protein structure shows the three-dimensional structure of protein. Users can drag, select, zoom in/out to view the structure, and also perform further operations through the toolbar on the right. This section also provides the download link of the structure file. It is worth noting that due to the limitations of computing power, only the three-dimensional spatial structure of the nonredundant proteins is currently provided.

The protein annotation shows the functional annotation results of homologous superfamily, family, domain, and unintegrated family/domain.

The location of proteins in the genome section shows the location of the protein in the genome to which it belong. The default view has been zoomed in to ensure that the protein is in the center of the view. Users can zoom in or out of the genome through the plus and minus signs in the upper right corner to view the positional relationship between the protein and other nearby genes. The red and orange in the upper part of the genome browser represent the reannotated ORFs, and the green and blue in the lower part represent the original ORFs (if present). Among them, red and green represent the forward ORFs, while orange and blue represent the reverse ORFs.

The protein sequence shows the amino acid sequence of the protein and provides the download link of the sequence file.

On the navigation page for evolutionary tree, users can enter different evolutionary tree pages by clicking on different card bars, which are distinguished based on the viral taxonomic level.

The page of the evolutionary tree consists of two parts: pre-constructed evolutionary tree and interactive evolutionary tree.

In the pre-constructed evolutionary tree, users can display or hide the evolutionary distance through buttons. In the evolutionary tree, genera or species are distinguished by color. The evolutionary tree shows the species and genotype of virus isolates, as well as the type and living habitat of their hosts or collection species, through color bands and color blocks.

In the interactive evolutionary tree, users can switch the display form of the evolutionary tree through buttons. Genera or species are also distinguished by color in the evolutionary tree. Users can perform operations such as highlighting, displaying the distance to the root, or reroot by clicking on nodes or evolving branches. Meanwhile, by clicking on the name of the virus isolate, users can be redirected to the detail page of the virus isolate.

Genomic collinearity page consists of two parts: genomic pairwise identity on the left and genomic collinearity on the right.

The genomic pairwise identity section presents the genomic pairwise identity from the complete iridovirus genomes through heat maps. Users can view high definition image on the new page by clicking the corresponding link.

In the genomic collinearity section, users can view the genomic collinearity between any two genomic sequences of iridovirus on the new page by searching or selecting.

On the navigation page for host range, users can enter different host range pages by clicking on different card bars, which are distinguished based on the viral taxonomic level, species classification, and degree of endangerment for species.

The host range is presented in the form of tables. Users can enter the content they want to retrieve in the search bar. The columns with sort buttons in the table header can be arranged in ascending or descending order by clicking. The toolbar includes functional buttons for full-screen display, selective display of certain columns, and reset of the table.

By clicking on the name of a host species, users can see a species summary introduction in a pop-up window, including a picture with copyright information and a brief introduction. Below the window, a link to Wikipedia ® is provided. By clicking on the taxonomic level link, users can go to view the host ranges of different viral subfamilies or genera, and clicking on the name of the virus species will go to that species in the dataset. Users can directly view the relevant reference by clicking on the reference link.

The tables contain the following contents:

On the navigation page for vaccine, users can enter different vaccine pages by clicking on different card bars, which are distinguished based on the vaccine type, viral taxonomic level, and host classification.

The vaccine is presented in the form of tables. Users can enter the content they want to retrieve in the search bar. The columns with sort buttons in the table header can be arranged in ascending or descending order by clicking. The toolbar includes functional buttons for full-screen display, selective display of certain columns, and reset of the table.

By clicking on the taxonomic level link, users can go to view the vaccine of different viral subfamilies or genera, and clicking on the name of the virus species will go to that species in the dataset. Users can directly view the relevant reference by clicking on the reference link.

The tables contain the following contents:

On the navigation page for visual detection method, users can enter different detection method pages by clicking on different card bars, which are distinguished based on the detection method type, viral taxonomic level, and host classification.

The visual detection method is presented in the form of tables. Users can enter the content they want to retrieve in the search bar. The columns with sort buttons in the table header can be arranged in ascending or descending order by clicking. The toolbar includes functional buttons for full-screen display, selective display of certain columns, and reset of the table.

By clicking on the taxonomic level link, users can go to view the detection method of different viral subfamilies or genera, and clicking on the name of the virus species will go to that species in the dataset. Users can directly view the relevant reference by clicking on the reference link.

The tables contain the following contents:

Users can download the genome, ORFs, and proteins sequence files of all virus isolates in IVCDB individually or in batches on the download page.

The download page is presented in the form of tables. Users can enter the content they want to retrieve in the search bar. The columns with sort buttons in the table header can be arranged in ascending or descending order by clicking. The toolbar includes functional buttons for full-screen display, selective display of certain columns, and reset of the table.

By clicking on the genome link, users can go to the corresponding external database. By clicking the download link, users can download the genome, ORFs, or proteins sequence files of a certain protein separately. Users can also select multiple proteins simultaneously on the far left of the table and then download the genome, ORFs, or proteins sequence files in batches through the "Download genome file", "Download ORFs file", or "Download proteins file" button in the toolbar.

The tables contain the following contents:

Users can report any bugs related to IVCDB, offer suggestions or make new feature requests on submit & feedback page. Users can also upload new virus genomes or any other information related to the Rainbow virus. We also warmly welcome any other related exchanges and discussions.