BALCONY (version 0.2.10)

create_structure_seq: Superimpose structural data of interest on sequence after the alignmment

Description

Create sequence of a protein structure model based on numbers of amino acids given in a text file (list of IDs and numbers in protein)

Usage

create_structure_seq(structure_list, sequence_id, alignment,
                     pdb_path = NULL, chain_identifier = NULL, shift = NULL)

Arguments

structure_list

A list of structure data used for further evolutionary analysis. It can be text file(s) read by the read_structure function (text file with 2 columns: numbers of amino acids and 3-letters codes of AA; First row needs to contain markers)

sequence_id

The id/name of the target sequence in alignment which will be a base of structure sequence

alignment

An alignment object read with read.alignment function, must contain the target sequence

pdb_path

A string specifying the path to the PDB file with structural information. Optional parameter, required if the structure is incomplete e.g. fragments such as loops are missing

chain_identifier

A character specifying the chain of interest e.g. "A" or "B"

shift

A numeric value. In case there is a need to adjust the amino acids numeration due to missing amino acids at the beginning of the structure (that are not considered in the PDB file REMARK465 section)

Value

structure_matrix

A matrix of characters "S" and "N" marking on sequence the structural element; "S" - amino acid forms the analyzed structure, "N" - amino acid which does not form the structure. Number of rows of the matrix corresponds to the number of structures analyzed

structure_numbers

A vector containing the numbers of the amino acids in the sequence of interest (no gaps)

structure_probabilities

A matrix of numeric values: probabilities of corresponding to the structural information from first element of the output, which helps to reduce the effect of non-consistent structural amino acids on the conservativity analysis of the structure of interest

Details

This function is useful to create sequence covered with structural data provided in a .txt file. This sequence can be compared with alignment to check the conservation for interesting amino acid(s). Additionally, if path to the PDB file is provided the function corrects the output accordingly to the information in REMARK465 on missing amino acids.

See Also

get_remarks465_pdb, find_consecutive_seq, read_structure, read.alignment

Examples

# NOT RUN {
data("alignment")
structure_files = c(system.file("extdata", "T1_4JNC.structure", package = "BALCONY"),
                    system.file("extdata", "T2_4JNC.structure", package = "BALCONY"),
                    system.file("extdata", "T3_4JNC.structure", package = "BALCONY")
                    )
structure_list = read_structure(structure_files)
#creating library uniprot - PDB
lib=list(c("Q84HB8","4I19","4QA9"),
        c("P34913","4JNC"),
        c("P34914","1EK2","1CR6","1EK1","1CQZ"))
pdb_name = "4JNC"
uniprot=find_seqid(pdb_name,lib)
tunnel=create_structure_seq(structure_list,uniprot,alignment)
# }