Closed Starfishgames closed 5 years ago
Hi Starfishgames,
Thank you very much for your interest in VirFinder.
Yes, in order to train the classifier both viruses (positive examples) and bacteria hosts (negative examples) are needed. VirFinder has the function for training models using users' database.
Hope that helps :)
Best wishes, Jie
Dear Jie, Thanks for your reply. So, bacterial sequences used for the training do not need to be the "real" host of the viruses I'm using for training, if I understand correctly. I might use, for instance, metagenomically-identified viral genomes for positive examples and prokaryotic genomes from the proGenomes database as a negative examples. Am I right? Thanks in advance
You are welcome!
Yes, you are right. The positive examples are viruses and negative examples are non-viruses such as prokaryotic genomes. In my paper, I used phages and prokaryotic genomes as my positive and negative examples. The hosts of the phages are prokaryotes, but they do not need to be corresponding to each other in the training dataset. All we need are a set of positive and a set of negative examples.
Best wishes, Jie
On Tue, Mar 27, 2018 at 3:40 AM, Starfishgames notifications@github.com wrote:
Dear Jie, Thanks for your reply. So, bacterial sequences used for the training do not need to be the "real" host of the viruses I'm using for training, if I understand correctly. I might use, for instance, metagenomically-identified viral genomes for positive examples and prokaryotic genomes from the proGenomes database as a negative examples. Am I right? Thanks in advance
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ca I train with a eukaryotic host genome, such as human?
I'd also like to know if you can train the model with a eukaryotic host genome.
Thank you for the interest in using VirFinder! (Sorry for my late reply)
It is possible to train VirFinder using viruses with eukaryotic host genomes. It is not known how well the model can predict. Since the size of the human genome is huge (compared to the amount of total viral sequences), I suggest to first downsample the human genome first. The program uses the equal amount of DNA bps for viral sequences and host sequences.
Dear all, I'm very interested in this tool. I'm actually trying to understand whether it's possible to expand the number of viral genomes to produce another training dataset by adding metagenomically-identified contigs representing putatively complete phage genomes from environmental datasets (e.g. Pacific Ocean Virome, Tara Oceans). Is the host gene sequence mandatory for creating the new model? Best regards