VIRUS_DB2.0
An Online Crowdsourcing Virus Database for Classification Based on Natural Vector
Q: How to submit a sequence?
A: For single sequence, you can copy the content from the FASTA file directly (with the first line beginning with ‘>’) to the ‘Sequence’ blank, OR to upload the file in the ‘FASTA File’. For multiple sequences, ONLY a FASTA file is accepted.
Q: Why the email says that no prediction is made?
A: Many reasons can cause this. First, VirusDB is based on the whole genome rather than segmented sequences of viruses. If the input is not the whole genome, the distance between the query virus and database is very likely to be very large so that we cannot make a reliable prediction. Second, the scale of our database may be a problem as well. The number of viruses studied and sequencing is growing explosively. Evidently, the larger and newer version of the database can lead to better and more persuasive results. Currently, our database has been continuously and automatically fetching NCBI data. So if you receive an email with no prediction, Please try our updated database later and we are devoted to making a reliable prediction for you.
Q: How do you make a prediction? What is the threshold?
A: Since every class/family has its own property, it is not wise to set up an absolute threshold for all label. Thus we introduce a .75 cut-off distance for every class/family. We only make a prediction when the distance between the query virus and the class/family is smaller than the cut-off. In this way, we decrease the error rate effectively. For more details, please see reference[3].
Q: Can I get the calculation result when there is no prediction?
A: In the current version, we don’t send the users about the nearest viruses calculated by our method if the
distance is larger than the .75 cut-off. It is possible that the query virus is in the same class/family with
the second or third nearest virus in the list of neighbors. However, since we cannot explain the heterology with
the nearest one, we don’t provide the result to users in the email. However, if you are interested in the
result, please contact yuwp_1985@163.com for more information.
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