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Frequently asked questions
1. May I use the figures from your website in my publications, presentations or website etc?
2. How can I know the update time/status of your database?
3. I found some VF (or other important information) missed in your database, what can I do?
4. Would you please send me the virulence factors data set of VFDB?
5. Where can I get a copy of all protein/DNA sequences from VFDB for local BLAST?
6. Why the new comparison tables cover additional VFs/genes? (Some VFs listed in the comparison tables offer links to related literatures in PubMed instead of detail description pages in VFDB, why?)
7. Oh, I found all/some plasmids from the genome of xxx were missed from your comparison table.
8. Why some released/published genomes were not included into your comparison table?
9. May I send you the entire pathogenomic table of my newly determined genome? How to do?


Q1: May I use the figures from your website in my publications, presentations or website etc?
A: All figures here can be used for non-profit purpose freely as long as you refer VFDB as origin or cite our publication. Commercial users should contact us for detail information. Note that some figures were reproduced from other literatures (citation information should present above the individual figures).

Q2: How can I know the update time/status of your database?
A: The last update time of VFDB is displayed at the bottom right of the main page. You can find the most up-to-date statistic information (summary and detailed tables) about VFDB in the status page. For current status of comparative results, you can visit the part of comparative pathogenomics of status page.

Q3: I found some VF (or other important information) missed in your database, what can I do?
A: Researchers are kindly invited and encouraged to deposit their new results about VFs at VFDB. Submission might either be performed through the feedback form or by email to yangj#ipbcams.ac.cn.

Q4: Would you please send me the virulence factors data set of VFDB?
A: We would always like to help users for academic research purpose. However, please note that the information in VFDB is not just a simple table that can be easily viewed in local tools such Excel. Actually it contains several independent tables with many cross-links. So we believe that the best way to view the content of VFDB is to access it via the CGI scripts we provided by your browser instead of download a local version. Of course, we can provide users a local version of our data, or any portion of it for local use, if you insist. But you'd better let us know what kinds of information you want. So we may prepare a special dataset (maybe a table) for you. Otherwise, it may puzzle you if we just send the dump of our database to you. Users can contact us through the feedback form or by email to yangj#ipbcams.ac.cn.
NOTE: a simplified copy of all virulence factors with related descriptions is monthly released in Excel format from the download page now.

Q5: Where can I get a copy of all protein/DNA sequences from VFDB for local BLAST?
A: We encourage users to use the web-blast service of VFDB to query by their own sequences since it offers direct links to individual genes pages in the result. However, the sequences in FASTA format are monthly released for local use from the download page if you need to process large amount of queries.

Q6: Why the new comparison tables cover additional VFs/genes? (Some VFs listed in the comparison tables offer links to related literatures in PubMed instead of detail description pages in VFDB, why?)
A: The previous release of VFDB covers only experimentally demonstrated VFs, however, by introducing the comparative genomics approaches the current release try to also include those genome predicted VFs for comparative analysis. That's one of the reasons of the additional VFs listed in the comparison table. Another reason is that the previous release usually chooses one representative pathvar/serotype of each genus for collection of VFs. Since genomes of various pathogens are available, some additional VFs need to be listed in the table for genome comparison. Anyway, we are updating the content to try to provide full information for all VFs ASAP.

Q7: Oh, I found all/some plasmids from the genome of xxx were missed from your comparison table.
A: Bacteria usually carry a set of plasmids, most of which are irrelated to virulence. Therefore, currently we include only those virulence-related plasmids in VFDB (i.e., those encode known or potential VF genes).

Q8: Why some released/published genomes were not included into your comparison table?
A: In general, we intend to include all publicly available genomes into the comparison table timely. Reasons for the missing genomes could be:
1) For convenience of later data storage and process, only genomes that are available from NCBI's RefSeq database can be analyzed by the current pipeline for comparison (both pathogenic and non-pathogenic isolates). We are sorry for those genomes only released from authors' own website or for any reason not be included in RefSeq.
2) The comparison tables are scheduled monthly update by monitoring information from the Complete Microbial Genomes webpage of NCBI. So newly released genomes will be included within a month. Please contact us if you have any urgent request.
3) Currently, we have difficulty to analyze a few of unpublished genomes of less documented species/subspecies or non-clinical isolates. We will include them once the relevant publications or sufficient background information are available. We will highly appreciate if the authors can send us the pathogenomic table of their new genomes (see Q9 for instruction).

Q9: May I send you the entire pathogenomic table of my newly determined genome? How to do?
A: Researchers are kindly invited and encouraged to send us the known or analyzed pathogenomic data of their new genomes. Please follow the steps bellow:
1) Go to the full comparison page of pathogenomic composition of the pathogen you are going to submit (click the genus of your pathogen in left menu, for example Listeria, and then click the underlined 'Comparative pathogenomics' link in the page).
2) Scroll down to the bottom of the page, click the download icon () and save the current table into Excel format.
3) Edit the Excel table, add column(s) for the new genome(s) and fill the cells with corresponding systematic ID (i.e. locus_tag in GenBank file) of the homolog if the VF genes present in the genome, or leave it blank if absent.
4) Save the table and send it to yangj#ipbcams.ac.cn.
We will validate your table content before load it to the database, and will contact the author if any conflicts found.