phmmer_2abl

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

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

For further details, see https://hmmer-web-docs.readthedocs.io/en/latest/appendices.html