phmmer_2abl: phmmer_2abl
In currocam/utilsHMMER: HMMERutils

phmmer_2abl

R Documentation

phmmer_2abl

Description

A DataFrame with 25 results of a phmmer search of the 2abl sequence.

Usage

phmmer_2abl

Format

A data frame with 49 variables:

algorithm: HMMER algorithm
uuid: unique hmmer identifier
stats.page
stats.nhits: The number of hits found above reporting thresholds
stats.elapsed
stats.Z: The number of sequences or models in the target database
stats.Z_setby
stats.n_past_msv
stats.unpacked
stats.nseqs
stats.user
stats.domZ_setby
stats.n_past_bias
stats.sys
stats.n_past_fwd
stats.total
stats.nmodels: The number of models in this search
stats.nincluded: The number of sequences or models scoring above the significance threshold
stats.n_past_vit
stats.nreported: The number of sequences or models scoring above the reporting threshold
stats.domZ: The number of hits in the target database
hits.archScore
hits.ph: Phylum
hits.arch
hits.kg: Kingdom
hits.ndom: Total number of domains identified in this sequence
hits.extlink
hits.fullfasta: Protein sequences as a character vector.
hits.taxid: The NCBI taxonomy identifier of the target (if applicable)
hits.acc: Accession of the target
hits.taxlink
hits.desc: Description of the target
hits.pvalue: P-value of the score
hits.flags
hits.nregions: Number of regions evaluated
hits.niseqs
hits.name: Name of the target (sequence for phmmer/hmmsearch, HMM for hmmscan)
hits.species: The species name of the target (if applicable)
hits.score: Bit score of the sequence (all domains, without correction)
hits.bias
hits.sindex
hits.nincluded: Number of domains satisfying inclusion thresholding
hits.domains: The domain or hit hash contains the details of the match, in particular the alignment between the query and the target.
hits.pdbs: Array of pdb identifiers (which chains information)
hits.evalue: E-value of the score
hits.nreported: Number of domains satisfying reporting thresholding
hits.archindex
hits.acc2: Secondary accession of the target