EnVhog - Download

Sequences and HMM data

enVhogs (protein clusters)

• HMMs (HHblits format) 13Gb
• MMSeqs2 profile database 6.3Gb

Raw data

• Viral contigs in fasta format 27Gb
• All proteins in fasta format 18Gb

Tables

• Annotation tables 1.7Gb: Tables describing contigs, enVhogs, taxonomy. More precisely, this archive contains (click to see header descriptions):
  contigs_infos_class.tsv: Info and taxonomy of contigs, number of enVhog of each category on each contig

  ID
  Contig
  Length: contig length in bp
  Source: data source (Collected/IMGVR/GLUVAB/eFAM/PHROGS/RefSeq_viral)
  nb.Proteins: number of proteins identified on the contig
  Taxonomy.rank
  Organism
  Taxonomy
  nbProti: Number of proteins on the contig
  nbEnv_c0_V: Number of enVhogs of category V on the contig at iteration 0
  nbEnv_c0_S: Idem with category S
  nbEnv_c0_U: Idem with category U
  nbEnv_c0_C: Idem with category C
  nbEnv_c3_V: Number of enVhogs of category V on the contig at iteration 3
  nbEnv_c3_S: Idem with category S
  nbEnv_c3_U: Idem with category U
  nbEnv_c3_C: Idem with category C
  envhog_infos.tsv: Infos and annotation of each enVhog

  enVhog: unique identifier
  prot: number of proteins in the enVhog
  dedup: number of deduplicated proteins in the enVhog
  shallow: number of shallow clusters in the enVhog
  standard: number of standard clusters in the enVhog
  pMaxLen: protein max length among cluster members
  pAvgLeng: protein average length
  pStdDev: standard deviation of protein lengths
  NEFF: Diversity of the cluster (average entropy of the alignment)
  bestPfamAc: PFAM accession number of PFAM best hit
  bestPfamId: PFAM Id of best PFAM hit
  bestPfamAn: PFAM Annotation of best PFAM hit
  bestPhrog: Phrog ID of best phrog hit
  bestPhrogAn: Phrog annotation of best phrog hit
  PhrogCat: Phrog category of best phrog hit
  bestKegg: Kegg gene ID of best kegg hit
  nbClades: Number of viral clades containing an homologous protein
  nbVir: Sum over clades of the proportion of viruses containing an homolog in each clade
  nbHost: Sum over specied of the proportion of hosts containing an homolog in each cellular species
  viralness: V_p
  hostness: C_p
  VQ: Viral quotient
  cat: Category U/S/C/V based on VQ and hostness
  hallmark: 1 if viral hallmark gene
  catMin: Category U/S/C/V based on VQmin and hostness
  catHall: Category U/S/C/V based on VQmin, hostness and hallmark gene (this category is used by the iterative algorithm)
  VQmin: Version of the VQ but with Cp shifted by 5%
  prot_dedup_shallow_standard_cluster_envhog_contig.tsv: Links between unique identifiers of proteins, contigs, shallow clusters, clusters and enVhogs.

  Protein ID
  Deduplicated representative ID
  Shallow cluster representative ID
  Standard cluster representative ID
  enVhog cluster representative ID
  contig ID
  
• enVhog categories 31Mb Classification of each enVhog using the Bayesian iterative algorithm
  See header

  envhog
  cluster_class_X: category V/C/S/U at iteration X
  lr_X: Log odd-ratio of category V vs category C at iteration X
  
• enVhog contig categories 31Mb Classification of each contig using the Bayesian iterative algorithm
  See header

  contig
  contig_class_X: category V/C/H/U at iteration X
  

Scripts

The scripts used to create the enVhog database can be found on this git repository.

Citation

When using this work please cite:

EnVhog: an extended view of the viral protein space on Earth Perez-Bucio R., Enault F., Galiez C. bioRxiv 2024.06.25.600602; doi: https://doi.org/10.1101/2024.06.25.600602

Contact: Clovis Galiez

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