This site is compatible with most major browser environments like Chrome, Safari and 360 (speed mode),etc. While the most updated 360 or Google Chrome is the most recommended. If you see the message "You are using a browser version with limited support for our site. For the best experience and full functionality, we recommend you use a more advanced Web browser" on the top of your page, update your browser or try another one.

Internet Explorer (IE) is NOT recommended. If you are using Internet Explorer (IE), make sure that your browser veision is greater than IE9, otherwise some functions cannot be implemented.

You can update your browser here:

• 360
• Google Chrome

Since all published data and services on our website are aviliable to all users, an account is NOT needed when enjoying our web service. For further cooperation, please CONTACT US: iginkgo@zju.edu.cn

A specific chromosome region on our website is represented by "chromosome:start site-end site". You can search for SNPs, genes and other informations in interested region in such format. Note that ginkgo has only 12 chromosomes. For example:

• 5:162020-163000

A number represented by scientific notation is recognizable on our website. You can use "E" for big numbers. For example, 1.2×10⁵ can be represented by 1.2E5:

• 5:300-1.2E5

To search for informations like SNP sites located in a specific gene is possiable. All genes from ginkgo genome are numered with five digits in format "Gb_×××××". For example:

• Gb_00306

All genes from ginkgo genome are numered with five digits in format "Gb_×××××". For example:

• Gb_00306

In this page, you can get general information about the gene and its exons. Both nucleotide sequence and protein sequence is provited in FASTA. Using the toolbar on the right of the page, you can launch a BLAST serch for this sequence conveniently. The expression level is also avilablen on this page.

A SNP site on our website is represented by "chromosome:site". For example：

• 5:26180

In this page, you can get general information about this variation site and associated genes.

Searching for SNPs in a specified chromosome region is recommended. You can specify a region in format "chromosome:start site-end site" or by Gene ID. Have a try:

• 5:20-2020
• 5:300-1.2E5
• Gb_35863

The filter toolbar is provided on the left of the page. You can also sort the results by location or quality.

The sequences can be downloaded in fasta. We provide a "download" button for each sequence in the gene and protein page. You can also download a sequence in Jbrowse page by double-click the gene. For example:

• In gene page: Gb00306
• In Jbrowse page: Gb00306

All published genetic data on our website are provided in FTP site. You can obtain those data with your browser or FTP client software via address https://ginkgo.zju.edu.cn/ftp/ or ftp://ginkgo.zju.edu.cn/ (may NOT supported by some browsers). A README file is provided in each directory, explaining the directory structure or data format.

Please be aware that some of these files can run to many gigabytes.

Starting with Chrome 80, Google began to abandon FTP support.In the current version of Chrome 81, FTP support is disabled by default. Therefore, you cannot open our FTP page: ftp://ginkgo.zju.edu.cn/. Here, we recommend several alternatives:

1. Use 360 browser that supports FTP.
2. Use a FTP client software, for example, FileZilla to connect ftp://ginkgo.zju.edu.cn/.
3. Try our HTTPS downloading site: https://ginkgo.zju.edu.cn/ftp/ that is supported by all browswes.

The blast task you submitted did not perform properly by ncbi-blast+ if you got the message "Sorry, your job failed to run". We recommend you reconfirm your sequence and the parameters, and try submitting your task again.

We have not encountered this situation when using blast normally. If the error recurs, please feel free to contact us.

Below are common reasons that a blast task results in the "No significant similarity found" message.

Short query sequences: Short alignments may have Expect values above the default threshold, which is 10 on most pages, and, therefore, are not displayed. Try increasing the Expect threshold (under "General options").

Filtering: Some of the BLAST programs mask regions of low complexity by default. These regions are not allowed to initiate alignments, so if your query is largely low complexity, the filter may prevent all hits to the database.

The result of your blast task would be stored on our server for five days. If you got the message "Sorry, the job does not exist or has expired", please make sure that the task ID is correct first. If you want the result submitted 5 days ago, we recommend you submit your task again and it will not take too much time.

If the result is vitally important for you and it is hard to submit your sequences again, you might contact us for data recovery, but there is NO guarantee that it will work.

The Expect value (E) is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise.

The lower the E-value, the more "significant" the match is. However, keep in mind that virtually identical short alignments have relatively high E values. This is because the calculation of the E value takes into account the length of the query sequence. For more details please see the calculations in the BLAST Course provided by NCBI.

You can make a heat map online on our site. By choosing samples and genes, a heatmap for gene expression level can be provided in 10 seconds. All genes from ginkgo genome are numered with five digits in format "Gb_×××××". Note that the heatmap must be plotted with at least 2 avilable values. when more than one samples are selected, you can choose to remove those genes whose expression level remain 0 in all selected samples.

You can launch a primer design process by click the "Primer3Web" tool on any sequence/protein page or input your sequence in Primer3Web Page.

The Official instruction manual is provided on our site. You might click any parameters on Primer3Web page to check its meaning or function.

We prepared a k-mer lists of Ginkgo biloba for pre-masking.

The k-mer lists for some frequently-used species are also avilable on our site. You can check the species list here .

Researchers who wish to use GinkgoDB are encouraged to cite with:

Kai-Jie Gu, Chen-Feng Lin, Jun-Jie Wu, Yun-Peng Zhao^* (2022) GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba. Database 2022, baac046