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Table 2. Description of the contents of the evidence file generated by the VMGAP

From: The Viral MetaGenome Annotation Pipeline (VMGAP): An automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

1 2 3 4 5 6 7 8 9
ID CDD_RPS Subject definition % cov % ident e-value   % ident  
ID ALL GROUP_PEP Subject ID Subject definition Query length Subject length % cov % ident e-value
ID ACLAME_PEP Subject ID Subject definition Query length Subject length % cov % ident e-value
ID SANGER_PEP Subject ID Subject definition Query length Subject length % cov % ident e-value
ID ENV_NT Subject ID Subject definition Query length Subject length % cov % ident e-value
ID ENV_NR Subject ID Subject definition Query length Subject length % cov HMM description e-value
ID FRAG_HMM HMM begin HMM end % cov Total e-value HMM accession HMM description HMM length
ID PFAM/TIGRFAM_HMM HMM begin HMM end % cov Total e-value HMM accession   HMM length
ID PRIAM EC Number e-value     HMM description  
ID ACLAME_HMM HMM begin HMM end % cov Total e-value HMM accession   HMM length
ID PEPSTATS Molecular weight Isoelectric point      
ID TMHMM Number predicted helixes       
ID SIGNALP signal pep cleavage site position      
  1. Fields 1 and 2 correspond to the protein identifier and a flag specific for each analysis, respectively. % cov, percent coverage; % ident, percent identity; CDD_RPS, RPS-Blast vs. CDD DB; ALLGROUP_PEP, Blastp vs. protein NR DB; ACLAME_PEP, Blastp vs. ACLAME protein DB; SANGER_PEP, Blastp vs. in-house viral metagenomic DB; ENV_NT, Tblastn vs. ENV_NT DB; ENV_NR, Blastp vs. ENV_NR DB; FRAG_HMM, HMM searches vs. local PFAM/TIGRFAM HMM DB; PFAM/TIGRFAM_HMM, HMM searches vs. global PFAM/TIGRFAM HMM DB; PRIAM, RPS-Blast vs. PRIAM profile DB; ACLAME_HMM, HMM searches vs. global ACLAME HMM DB; PEPSTATS, peptide statistics; TMHMM, transmembrane domain searches; SIGNALP, signal peptide searches.