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Table 1 Features used in this study for the prediction of pVOG-pVOG functional association

From: Finding functional associations between prokaryotic virus orthologous groups: a proof of concept

Name Description
Co-occurrence Calculated by dividing the number of genomes where both pVOGs have hits by the total number of genomes where either of the pVOGs have hits (Jaccard similarity)
Average distance Minimum distance in nucleotides of the alignment envelopes (sensu hmmsearch) between the two pVOGs, averaged across all common genomes
Co-orientation Fraction of hits where both pVOGs are found on the same strand
Convergent orientation Fraction of hits where both pVOGs are found on opposite strands with 3’ ends facing each other
Divergent orientation Fraction of hits where both pVOGs are found on opposite strands with 5’ ends facing each other
Mean ANI Average Nucleotide Identity (ANI) of all genome pairs where the pVOGs co-occur, calculated with fastANI [26]
Mean AAI Average Amino acid Identity (AAI) of all genome pairs where the pVOGs co-occur, calculated with CompareM [27]
  1. All features except co-occurrence are calculated on genomes where both pVOGs have a significant hit