Selection can be deselected by clicking on the pillboxes, and multiple concurrent selections are supported. Enter a host name or taxid to the text box and several host terms will be suggested only 20 top taxids will be shown. Select the desired host term and hit Enter. The results will be restricted to sequences in the database with the indicated host term.
Multiple hosts can be filtered on simultaneously by adding additional host terms to the filter. Parsed terms are mapped to a standardized vocabulary, which was derived by curators by aggregating the variety of terms in GenBank files. Common mis-spellings are also included in this mapping strategy.
For example, "Accipter cooperii" is mapped to "Accipiter cooperii". The terms for isolation hosts are displayed in the host column of the results table.
If both isolation host and laboratory host can be mapped, only isolation host will be presented in the table host column. To search for sequences submitted by a particular author s enter the author's last names with or without initials. The terms for isolation source are parsed from the isolation source field in a sequence's GenBank record.
Examples of parsed terms are serum and plasma , which are all mapped to the standardized vocabulary term blood. Common mis-spelling as well as regional spelling differences are included in the mapping strategy. Multiple terms can be selected. Collection date From, To - is the collection date for the sample from which the sequence was derived. Environmental source filter allows to select virus sequences isolated from the environmental sources.
Select Include - to include all sequences isolated from environmental sources to the results table. Select Exclude - to exclude all sequences isolated from environmental sources to the results table. Lab host filter allows to view laboratory isolated virus sequences. Select Include - to include all laboratory isolated virus sequences to the results table. Select Exclude - to exclude all laboratory isolated virus sequences to the results table. Vaccine strains filter allows to find virus vaccine strain sequences.
Select Include - to include all virus vaccine strain sequences to the results table. Select Exclude - to exclude all virus vaccine strain sequences to the results table. This will open selection menu. To select all viral sequences, enter and then select the term viruses. Click on the Nucleotide tab to access genomic sequences, or the Protein tab to access amino acid sequences for individual proteins. In virus search results table you can compare search results in tabular display using the following sortable default columns :.
Host — virus isolation host Read more about isolation source vocabulary mapping here. In order to provide free and easy access to genome and protein sequences and associated metadata from the SARS-CoV-2, we created a dedicated Severe acute respiratory syndrome coronavirus 2 data hub. Bacteriophages include virus groups with the following NCBI Taxonomy IDs: , , , , , , , , , , , Select the desired popular virus searches group button located beneath the text box. Both options will open the tabular display with the information about viruses from selected group.
Learn more how to compare results in tabular display , build multiple sequence alignment of selected results , build phylogenetic tree of selected results or refine tabled results via filters. In case if nucleotide or protein sequence data were selected in Step 1, the default FASTA definition line will be presented in the format accession GenBank title and will include the GenBank sequence accession number and GenBank title:. You can change this default defline to fit your own needs by selecting Build custom sequence title option.
If in Step 1 you selected the Results Set the result of the current table view in CSV format, the downloaded results will show all selected columns data. You can modify the selected columns and choose the columns you need in Step 3: Select columns to include in results set. It may be used to identify data trends and select specific subsets of the data based on these trends.
By clicking on each statistic button, you will be referred to the corresponding sequences displayed in table form. The results can be further refined for various sequence attributes metadata via filters available on the results page learn more here. Virus taxonomy can be explored via an interactive sunburst chart.
The default view represents the classification for all available NCBI viral taxa. Only 4 levels of the whole hierarchy are visible on the plot at a given time.
To explore virus taxonomy, click on any slice section of any layer on the sunburst chart. This will trigger the plot to zoom into the selected taxa and display any additional taxa below the selection. Each viral taxa name is displayed on a corresponding slice or can be viewed in the hover-over tool-tip by placing your cursor over the slice. Dynamic breadcrumbs with viral taxa names are located above the sunburst plot. Breadcrumbs are also a secondary navigation system that show the location of the taxa in the hierarchy and clicking on one will refocus the plot on the selected taxa.
You can also see breadcrumbs by hovering over any slice in the sunburst. Clicking on the center of the sunburst chart will return you to the parent taxa. After selecting a specific taxonomy group on sunburst chart, you can view and explore the updated statistics in the top row of the dashboard. The interactive Host Distribution chart shows the distribution of virus host species. Each host bar is proportional to the number of virus sequences isolated from this host.
The total number of virus sequences for each bar can be viewed by hovering over the bar. To select a host species, click on a bar or on a corresponding host name. This will highlight selected host, as well as all virus taxonomy groups containing sequences isolated from the selected host. Only one host can be selected at a time. Clicking on the selected host a second time will de-select it or you can use the Reset option available in the top right corner of the host chart.
The statistics in the top row of the dashboard will be updated based on the selected host. Yes No. Sorry this didn't help. Thanks for your feedback. This thread is locked. You can follow the question or vote as helpful, but you cannot reply to this thread. I have the same question Report abuse. Details required :. Cancel Submit. Wungraileng Vashi. Hi, Thank you for posting your query in Microsoft Community. I understand how frustrating this must have been, I will try my best to help resolve this issue.
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