This uPOGs database was built in June, 2016 using the same method in Kristensen et al. Compared to the previous POGs database by Kristensen et al released in 2012, we gained more POGs. For more details, please refer to the help webpage of VirMiner website (http://147.8.185.62/VirMiner/help.php)
This ftp site contains the following information:

1.updated_POG_seqs.filtered.annotation.fa: the sequence of all POGs in FASTA format.

2.updated_POG.VQ0.8.fa: the sequence of the POGs with VQ 0.8 in FASTA format. VQ (virus quotient) was measured as the quotient of the frequency of matches to viral genomes (VQ = v/ (v+h),v:number of viral genomes matched /total number of viral genomes; h: number of prokaryotic genomes matched/total number of prokaryotic genomes). If one POGs has higher VQ, this POG is highly virus-specific.

3.POG_2016_VQ0.8.list: the gene id of the POGs with VQ 0.8.

4.VQ_for_POG.txt: VQ was given for each POG in this file. The first column refers to POG id, the second column refers to VQ.

5.POG_taxonomy_precision100_recall85_VQ0.85.single_copy.txt: The list of taxon-specific POGs was selected under the criteria: 100% precision, recall greater than 85%, VQ greater than 85% and present in at most a single copy per virus. These taxon-specific POGs could be used for quantitative analysis of the taxonomy level for phage annotation. The format was described from first to last colunmn: POG id, taxon id, taxonomy name, rank.

6.POG_taxonomy_precision100_recall100_VQ1.single_copy.txt: we also provided the more strict criteria for choosing taxon-specific POGs: 100% precision, 100% recall, VQ threshold at 1.0 and present in at most a single copy per virus.


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Reference
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Kristensen, D. M., Waller, A. S., Yamada, T., Bork, P., Mushegian, A. R., & Koonin, E. V. (2013). Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. Journal of bacteriology, 195(5), 941-950.


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Contact
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If you have any questions about the format and usage of these files, please contact: Tingting Zheng (tingting.zheng@hku.hk)