Cross-animal comparative analyses
VIRUSES & SEQUENCES
Cross-animal comparative analyses
Users can choose certain virus then click 'Go to analyse' button or click any node to perform comparative analyses on certain virus as well as related geographic distribution, host range and sampling time cross the animals housed in ZOVER.
Users can choose certain time period then click 'Go to analyse' button or click any node to perform comparative analyses on involved viruses,related geographic distribution,host range cross the animals housed in ZOVER.
Users can click any country to perform comparative analyses on involved viruses realted hosts and sampling time cross the animals housed in ZOVER.
Users can click 'Click to customize the hosts' button to perform comparative analyses on involved viruses realted geographic distribution and sampling time cross the animals housed in ZOVER.
VIRUSES & SEQUENCES
There are two ways as following: (i) click one of buttons in the menu panel of 'Browse certain animal-assosicated viruses' on the Home page, or (ii) click the 'Browse by virus' tab on the mainTable second page. This will bring a new Tab in the main content panel with information of known viruses families (genome type, average size).
Each line in the main table is expandable by single click the leading '+' icon or double-click the line itself. For easy visualizing the genome organization of the virus, a colorful linear map is offered for each COMPLETE viral sequence. Click the linear map will pop up a window within the webpage showing the linear map with detailed annotation information and direct links to individual records in GenBank.
It may be difficult to load too many lines in a single page especially for visitors with poor network speed or limited CPU power. So to avoid potential overloading we set to show 20 sequences per page in the information table by default. Users can use the navigation tools on the bottom tool bar of the table to view next or any other page.
For advanced users, searching the database would be a more efficient way to find required information than browsing the database. So we provide a powerful text search engine in the search panel. To show the search panel, click the 'Text Search' icon on the Home page or click the 'Search' button on the top toolbar of the window. For quick start, users can use the 'Quick search' form that contains a single entry. The 'Advanced search' form allows users to perform customized complex searches of all information in the database.
For each information table, a 'Download sequence(s)' button is available on the top tool bar. Click the button will show a menu to allow users to save all sequences (in the current table view) or selected sequence (single click to select a line) into nucleotide/protein sequences in FASTA format.
Single click the 'BLAST search & phylogenetic analysis' icon on the Home page or click the 'Search' button on the top toolbar of the window. Please note that users can set to search in all sequences in ZOVER or only complete genomes using BLAST.
In order to make phylogenetic analyses users MUST perform BLASTN or BLASTP search (see above) first to determine which sequences in the database should be included. In the Tab of BLAST result a 'Phylogeny' button is given at the bottom right. Click the button will bring a pop up window to allow users to select sequences for follow-up phylogenetic analyses (note that the user input sequence for BLAST MUST be included). After user selections just submit the form and an integrated pipeline for multiple sequence alignment and tree construction will be processed in background. Users will have a message window with an ID (8-bit integer). Users can input the ID into the entry at the bottom left of the window and click the button to retrieve the tree later. Both multiple sequence alignment and phylogenetic tree can be saved as local files for further analyses.
There are two ways as following: (i) click one of buttons in the menu panel of 'Browse certain animal-assosicated viruses' on the Home page, or (ii) click the 'Browse by rodent/chiroptera/mosquito/tick' tab on the mainTable second page.For brevity, the taxonomic tree shows to only family level, but it can be further expanded to genus/species level by single click the branch of the tree.
To bridge the gaps between virologists and zoologists the basic information of hosts such as species, common name, known distribution can be easily browsed when users choose to browse all viruses by host (see above). Note that to avoid possible overloading of the client web browser, the information is displayed with 10 host species per page by default. For quick locating a certain species, users can use the search entry at the top toolbar for searching by host name/distribution. Click the host name in the search results can also bring the Tab with all viruses identified in this type of host.
The detailed phylogenetic relationships between different hosts were retrieved from previous studies and carefully integrated into the database. Users can click the 'Host phylogeny' on the top toolbar of the window to open the hosts phylogeny Tab showing the hosts super tree in the main content panel. Then click the families or species in the figure will show detailed sub-trees. Or alternatively, when browse the hosts information (see above) users can click the tree icon shown below the hosts' name to show the sub-tree directly with this host species underlined. Please note, the hosts phylogenetic information is also searchable by using the search entry at the top toolbar of the hosts phylogeny Tab.
For easy further offline analyses the each information table can be saved as local Excel file using the 'Save this table' button or 'Save selected' button at the top tool bar of the main table.
We provide a highly intuitive and responsive user interface, so the information table is fully sortable and filterable. To sort the table using certain column values ascendingly users can single click the column title. Click the column title again will change to sort the table by the column values descendingly.To filter the table by certain column values users need to input key words in input box at the top tool bar of the main table.
We provide a highly intuitive and responsive user interface, so the information table is highly configurable.To hide or show some columns, users can mouse over 'Toggle Column' button to choose hide or show certain column.
Single click the 'Live data statistics' icon on the Home page or the 'Statistics' button on the top toolbar of menu panel will bring a new window showing the current statistical charts of all data in the database, including current identified viruses sequences available in GenBank each year, publications report current identified viruses sequences in PubMed each year, and a set of interesting pie charts. These statistic charts are based on live data in the backgroud database, and the data last update time is showed on subtitle of the window. Please note that all pie charts have a configure button on the top left corner for setting different region/family/diet etc.
The aforementioned statistical charts are designed for ALL data in the database. For easy analyses each information table allows users to make customized statistical charts on some columns, including viral family, host species, host family, sample type, and sampling country. Users need to mouse over 'Show pie' button first and click the arrow at the right ride of the column title. So a pop up window with an animated pie chart of the column values will be presented. Users can mouse over each piece to view details of the information. Please note that the pie chart includes ONLY the lines shown in the current table. So if filter or paging exists in the table the pie chart displayed would not include the lines been filtered out or not shown this page. Thus, make sure to clear filters and turn off the paging setting if users hope to make statistical charts on full dataset.
For convenient regional virus analyses, a tree with a geographic category organized by continents and countries is provided in the second page. Single click the 'Browse rodent/bat/mosquito/tick-assosicated viruses' buttons on the Home page or the 'Browse by region' tab on the second page.Please note that the markers indicate countries only instead of the accurate location.
After opening the table of interested subset (either by browse or by search the data), users can click the 'Global map' item in the appeared menu to view the world map with markers indicating the distributed countries of listed sequences. Please note that it shows the distribution of ONLY the lines shown in the current table. So if filter or paging exists in the table the distribution map displayed would not include the lines been filtered out or not shown in the page. Thus, make sure to clear filters and turn off the paging setting if users hope to make statistical charts on full dataset.
For easy navigation the multifunctional menu panel is shown on the left side by default. For maximize the visible region of the main content panel users can easily collapse the menu panel by clicking the 'Close Main Menu' button on the top of the menu panel. To restore the menu panel users can single click the 'Open Main Menu' button on the top of the menu panel.
Please feel free to contact Dr. Jian Yang for any further questions or comments about the database.