IVDB Database Search Help

For simple database search

1. What's in our database

IVDB contains viral type/subtype, source information, nucleotide/protein sequence (complete genome, CDS, UTR, three-dimensional (3-D) structural data), sequence alignment, polymorphism, and categorized literature and web resources covering the IV genomics, pathogenicity and epidemiology. In the Search page, users can access all data hosted in IVDB and retrieve a combination of different data types by setting various search options. In the Search Result page, IVDB provides links to the detailed sequence reports and direct access to the IVDB-embedded analysis tools. All searching results can be selectively saved to a personalized WorkSet for users'convenience in data management. Users may maintain the WorkSet by themselves, delete, append or download the data as well as apply the data to successive analysis by using the provided tools.

2. General search guide

  • The main search interface is straightforward: select your criteria, press and hold 'Ctrl' for multiple selection.

  • If you choose the option 'Genome Set', the result will be returned only if all the segments are available.

  • At least one flu species must be selected.

  • The option 'Year' should be within the range of 1902 to 2006.

  • The option 'Length' should be a positive number.

    3. About the WorkSet

  • To facilitate your search and analysis, your can store your personal data in WorkSet .

  • Your work set will be unavailable if you idle for 2 hours in the web pages. After that, your WorkSet will be reset and everything in your work set will be lost. As long as you kept using IVDB,your work set will kept alive.

  • Once your search has completed, you can add the accession number to your current WorkSet by ticking the checkbox in front of it and click 'Add to WorkSet'.

  • The data in your WorkSet can be used directly by subsequent analysis tools such as blast, multi-alignment and to build phylogenetic tree. You can also download it as a standard fasta file.

    4. About the Search Result Page

  • To view the details of each entry, click the corresponding accession number.

  • The same color of adjacent items indicates they are from the same strain.

  • From the search results, you can use the links of Result Statistics & Secondary Search to get the statistical information of your search results. You can also perform the secondary search to refine your primary search results and acquire even more targeted data sets.

  • 5. Search Example

    For example, you may query influenza A virus sequences isolated from avian in China by setting 'type'=A, 'host'=Avian and 'country'=China.

    1) Click on the 'Search' button, you will receive the search result page as illustrated below in Figure 1. Click on the 'Distribution' button (as highlighted in red in Figure 1) to generate a world map of type A IV sequence distribution.

    2) Click on China on the world map to see the zoom-in map of sequence distributions in China. When placed cursors on Guangdong Province of China, it will show sequence statistics in the area with information on hosts and years of sampling (Figure 2).

    3) When clicked on the Guangdong Province, it will display a list of hyperlinked sequence records that allow users to view more details. If you only want to get the "HA" segment, click on "Result Statistics & Secondary Search" to further refine your data (Figure 3).

    4) If you want to download, BLAST, perform multiple sequence alignment or draw phylogenetic trees, select the data of interest and save them in your WorkSet. You may view or modify your WorkSet data and apply them to the analytical tools (Figure 4).

    Figure 1

    Figure 2

    Figure 3

    Figure 4

    IVDB is supported by institutional grant from Beijing Institute of Genomics, CAS  Feedback