extract_from_HMMER_data_tbl: A function that extracts information from 'HMMER_data_tbl',...

In currocam/taxa2hmmer: Get more out of homologous sequence search with HMMER

A function that extracts information from HMMER_data_tbl, allows to perform some common tasks and returns a Tidy DataFrame.

Description

A function that extracts information from HMMER_data_tbl, allows to perform some common tasks and returns a Tidy DataFrame.

Usage

extract_from_HMMER_data_tbl(
  HMMER_data_tbl,
  id_column = NULL,
  remove_redundancy = FALSE,
  annotate_taxonomic = NULL,
  evalue = NULL,
  calculate_physicochemical_properties = NULL
)

Arguments

HMMER_data_tbl	A DataFrame of subclass HMMER_data_tbl, obtained through the search family of functions or read_hmmer_from_xml.
id_column	A character vector with as many elements as rows in HMMER_data_tbl and that will be used to create the id column.
remove_redundancy	A Boolean, if TRUE then entries corresponding to 100% redundant sequences will be removed in sequence.
annotate_taxonomic	A character vector of one, if "local" is selected, an annotation will be made using a local database, while if "remote" is selected, it will be made using remote resources (slower).
evalue	A numeric vector of one, by default NULL. If a number is given, hits will be filtered according to that evalue.
calculate_physicochemical_properties	A Boolean, if TRUE a series of numerical descriptors will be calculated for each sequence.

Value

A DataFrame of subclass HMMER_data_tbl_tidy. It has as many rows as identified domains.

Sequence data structure

Variables beginning with "hits." have been extracted from the hash corresponding to the sequences. Remember that there are as many rows as there are domains identified, not per sequence. Therefore, these variables will be duplicated, for example, for a sequence in which 2 domains are identified.

• hits.name: Name of the target (sequence for phmmer/hmmsearch, HMM for hmmscan).

• hits.acc: Accession of the target.

• hits.acc2: Secondary accession of the target.

• hits.id: Identifier of the target.

• hits.desc: Description of the target.

• hits.score: Bit score of the sequence (all domains, without correction)

• hits.pvalue: P-value of the score.

• hits.evalue: E-value of the score.

• hits.nregions: Number of regions evaluated.

• hits.nenvelopes: Number of envelopes handed over for domain definition, null2, alignment, and scoring.

• hits.ndom: Total number of domains identified in this sequence.

• hits.nreported: Number of domains satisfying reporting thresholding.

• hits.nincluded: Number of domains satisfying inclusion thresholding.

• hits.taxid: The NCBI taxonomy identifier of the target (if applicable).

• hits.species: The species name of the target (if applicable).

• hits.kg: The kingdom of life that the target belongs to - based on placing in the NCBI taxonomy tree (if applicable).

Domain data structure

Variables beginning with "domains." have been extracted from the hash domains.

• domains.ienv: Envelope start position.

• domains.jenv: Envelope end position.

• domains.iali: Alignment start position.

• domains.jali: Alignment end position.

• domains.bias: null2 score contribution.

• domains.oasc: Optimal alignment accuracy score.

• domains.bitscore: Overall score in bits, null corrected, if this were the only domain in seq.

• domains.cevalue: Conditional E-value based on the domain correction.

• domains.ievalue: Independent E-value based on the domain correction.

• domains.is_reported: 1 if domain meets reporting thresholds.

• domains.is_included: 1 if domain meets inclusion thresholds.

• domains.alimodel: Aligned query consensus sequence phmmer and hmmsearch, target hmm for hmmscan.

• domains.alimline: Match line indicating identities, conservation +’s, gaps.

• domains.aliaseq: Aligned target sequence for phmmer and hmmsearch, query for hmmscan.

• domains.alippline: Posterior probability annotation.

• domains.alihmmname: Name of HMM (query sequence for phmmer, alignment for hmmsearch and target hmm for hmmscan).

• domains.alihmmacc: Accession of HMM.

• domains.alihmmdesc: Description of HMM.

• domains.alihmmfrom: Start position on HMM.

• domains.alihmmto: End position on HMM.

• domains.aliM: Length of model.

• domains.alisqname: Name of target sequence (phmmer, hmmscan) or query sequence(hmmscan).

• domains.alisqacc: Accession of sequence.

• domains.alisqdesc: Description of sequence.

• domains.alisqfrom: Start position on sequence.

• domains.alisqto: End position on sequence.

• domains.aliL: Length of sequence.

Taxonomic data structure

If annotate_taxonomic = "local" or annotate_taxonomic = "remote" is selected, as many columns as available taxonomic categories will be included. All of them will have in common that they will start with "taxa".

Theoretical physicochemical properties data structure

If calculate_physicochemical_properties = TRUE the following columns will be included. All of them will have in common that they will start with "properties".

• properties.molecular.weight: sum of the masses of each atom constituting a molecule (Da) using the same formulas and weights as ExPASy's.

• properties.charge: net charge of a protein sequence based on the Henderson-Hasselbalch equation using Lehninger pKa scale.

• properties.pI: isoelectric point calculated as in EMBOSS PEPSTATS.

• properties.mz: mass over charge ratio (m/z) for peptides, as measured in mass spectrometry.

• properties.aIndex: aliphatic index of a protein. The aindex is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins.

• properties.boman: potential protein interaction index . The index is equal to the sum of the solubility values for all residues in a sequence, it might give an overall estimate of the potential of a peptide to bind to membranes or other proteins as receptors, to normalize it is divided by the number of residues. A protein have high binding potential if the index value is higher than 2.48.

• properties.hydrophobicity: GRAVY hydrophobicity index of an amino acids sequence using KyteDoolittle hydophobicity scale.

• properties.instaIndex: Guruprasad's instability index. This index predicts the stability of a protein based on its amino acid composition, a protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable.

• properties.STYNQW: Percentage of amino acids (S + T + Y + N + Q + W)

• properties.Tiny: Percentage of amino acids (A + C + G + S + T)

• properties.Small: Percentage of amino acids (A + B + C + D + G + N + P + S + T + V)

• properties.Aliphatic: Percentage of amino acids (A + I + L + V)

• properties.Aromatic: Percentage of amino acids (F + H + W + Y)

• properties.Non-polar: Percentage of amino acids (A + C + F + G + I + L + M + P + V + W + Y)

• properties.Polar: Percentage of amino acids (D + E + H + K + N + Q + R + S + T + Z)

• properties.Charged: Percentage of amino acids (B + D + E + H + K + R + Z)

• properties.Basic: Percentage of amino acids (H + K + R)

Examples

## Not run: 
data <- search_phmmer(seqs = "FQTWEEFSRAAEKLYLADPMKVRVVLKYRH",
   dbs = c("swissprot", "uniprotrefprot", "ensembl"),
   verbose = TRUE)
df <- extract_from_HMMER_data_tbl(
   data,
   id_column = c("Swissprot", "Reference proteomes", "Ensembl"),
   remove_redundancy = TRUE,
   annotate_taxonomic = "local")

## End(Not run)

currocam/taxa2hmmer documentation built on April 10, 2022, 11:02 a.m.