cons2seqs_sim {BALCONY}R Documentation

Group consensus to each sequence in the alignment similarity

Description

The function calculates similarity of group consensus to each sequence in the alignment. It facilitates an assessment of consensus accuracy and identification of outlying sequences in the alignment. Grouping amino acids allows to check similiarity between sequences by amino acids properties of user's choice.

Usage

cons2seqs_sim(grouped_alignment, grouped_consensus_seq)

Arguments

grouped_alignment

The output of read.alignment function

grouped_consensus_seq

A string of amino acids, the output of consensus function

Details

AA in consensus sequences and aligned sequences are converted into groups symbols according to method of user's choice. Returned values are percentage of similar amino acids considering the properties in consensus sequence and aligned sequence.

Value

percentage

numeric vector of identity score (percentage); positions in the numeric vector correspond to sequences in alignment, respectively

Author(s)

Alicja Pluciennik & Michal Stolarczyk

See Also

read.alignment, consensus, align_params

Examples

data("small_alignment")
alignment = delete_isoforms(small_alignment)
threshold_consensus = 30
grouping_method = "substitution_matrix"
alignment_grouped = align_seq_mtx2grs(alignment2matrix(alignment),grouping_method)
consensus_seq_grouped = consensus(alignment_grouped, threshold_consensus)
consensus_to_seqs_similarity = cons2seqs_sim(alignment_grouped, consensus_seq_grouped)

[Package BALCONY version 0.2.10 Index]