Base coordinates on a given Abelian group representation
Given a string denoting a codon or base from the DNA (or RNA) alphabet, function base_coord returns the base coordinates in the specified genetic-code Abelian group, as given in reference (1).
DNA sequences to GRanges of bases.
Function seq2granges transform an object from
DNAStringSet,
DNAMultipleAlignment-class or a character into
an object from BaseSeq.
BaseSeq-class object to DNAStringSet-class object.
Function base_seq2string_set transforms an object from
BaseSeq into an object from
DNAStringSet-class.
Usage
base_coord(base = NULL, filepath = NULL, cube = "ACGT", group = "Z4", ...)
# S4 method for class 'DNAStringSet_OR_NULL'
base_coord(
base = NULL,
filepath = NULL,
cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
"ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
"CTGA", "GACT", "GCAT", "TACG", "TCAG"),
group = c("Z4", "Z5"),
start = NA,
end = NA,
chr = 1L,
strand = "+"
)
seq2granges(base = NULL, filepath = NULL, ...)
# S4 method for class 'DNAStringSet_OR_NULL'
seq2granges(
base = NULL,
filepath = NULL,
start = NA,
end = NA,
chr = 1L,
strand = "+",
seq_alias = NULL,
...
)
base_seq2string_set(x, ...)
# S4 method for class 'BaseSeq'
base_seq2string_set(x)
base_matrix(base, ...)
# S4 method for class 'DNAStringSet_OR_NULL'
base_matrix(
base,
cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
"ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
"CTGA", "GACT", "GCAT", "TACG", "TCAG"),
group = c("Z4", "Z5"),
seq_alias = NULL
)Arguments
- base
An object from a
DNAStringSetorDNAMultipleAlignmentclass carrying the DNA pairwise alignment of two sequences.- filepath
A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
- cube
A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
- group
A character string denoting the group representation for the given base or codon as shown in reference (1).
- ...
Not in use yet.
- start, end, chr, strand
Optional parameters required to build a
GRanges-class. If not provided the default values given for the function definition will be used.- seq_alias
DNA sequence alias/ID and description.
- x
A 'BaseSeq' class object.
Value
Depending on the function called, different object will be returned:
Function 'base_coord'
This function returns a BaseGroup-class object
carrying the DNA sequence(s) and their respective coordinates in the
requested Abelian group of base representation (one-dimension, "Z4" or
"Z5"). Observe that to get coordinates in the set of integer numbers
("Z") is also possible but they are not defined to integrate an Abelian
group. These are just used for the further insertion the codon set in the
3D space (R^3).
Function 'seq2granges'
This function returns a BaseGroup object carrying the DNA
sequence(s), one base per ranges. A BaseGroup object inherits
from GRanges-class.
Function 'base_seq2string_set'
This function returns a DNAStringSet-class.
A BaseGroup-class object.
Details
Function 'base_coord'
Function base_coord is defined only for pairwise aligned sequences. Symbols "-" and "N" usually found in DNA sequence alignments to denote gaps and missing/unknown bases are represented by the number: '-1' on \(\mathbb{Z}_4\) and '0' on \(\mathbb{Z}_5\). In \(\mathbb{Z}_{64}\) the symbol 'NA' will be returned for codons including symbols "-" and "N".
References
Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543
M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.
R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.
Author
Robersy Sanchez https://genomaths.com
Examples
## Example 1. Let's get the base coordinates for codons "ACG"
## and "TGC":
x0 <- c("ACG", "TGC")
x1 <- DNAStringSet(x0)
x1
#> DNAStringSet object of length 2:
#> width seq
#> [1] 3 ACG
#> [2] 3 TGC
## Get the base coordinates on cube = "ACGT" on the Abelian group = "Z4"
base_coord(x1, cube = "ACGT", group = "Z4")
#> BaseGroup object with 3 ranges and 4 metadata columns:
#> seqnames ranges strand | seq1 seq2 coord1 coord2
#> <Rle> <IRanges> <Rle> | <character> <character> <numeric> <numeric>
#> [1] 1 1 + | A T 0 3
#> [2] 1 2 + | C G 1 2
#> [3] 1 3 + | G C 2 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Example 2. Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln
#> DNAStringSet object of length 2:
#> width seq
#> [1] 51 ACCTATGTTGGTATT---GCGCTCCAACTCCTTGGCTCTAGCTCACTACAT
#> [2] 51 ATCTATGTTGGTATTACGACGCTCCAATTCCTTGGGTCC------CTCCTT
## DNA base representation in the Abelian group \eqn{\mathbb{Z}_4}
bs_cor <- base_coord(
base = aln,
cube = "ACGT"
)
bs_cor
#> BaseGroup object with 51 ranges and 4 metadata columns:
#> seqnames ranges strand | seq1 seq2 coord1 coord2
#> <Rle> <IRanges> <Rle> | <character> <character> <numeric> <numeric>
#> [1] 1 1 + | A A 0 0
#> [2] 1 2 + | C T 1 3
#> [3] 1 3 + | C C 1 1
#> [4] 1 4 + | T T 3 3
#> [5] 1 5 + | A A 0 0
#> ... ... ... ... . ... ... ... ...
#> [47] 1 47 + | T T 3 3
#> [48] 1 48 + | A C 0 1
#> [49] 1 49 + | C C 1 1
#> [50] 1 50 + | A T 0 3
#> [51] 1 51 + | T T 3 3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Example 3. DNA base representation in the Abelian group \eqn{\mathbb{Z}_5}
bs_cor <- base_coord(
base = aln,
cube = "ACGT",
group = "Z5"
)
bs_cor
#> BaseGroup object with 51 ranges and 4 metadata columns:
#> seqnames ranges strand | seq1 seq2 coord1 coord2
#> <Rle> <IRanges> <Rle> | <character> <character> <numeric> <numeric>
#> [1] 1 1 + | A A 1 1
#> [2] 1 2 + | C T 2 4
#> [3] 1 3 + | C C 2 2
#> [4] 1 4 + | T T 4 4
#> [5] 1 5 + | A A 1 1
#> ... ... ... ... . ... ... ... ...
#> [47] 1 47 + | T T 4 4
#> [48] 1 48 + | A C 1 2
#> [49] 1 49 + | C C 2 2
#> [50] 1 50 + | A T 1 4
#> [51] 1 51 + | T T 4 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Example 4. Load a multiple sequence alignment (MSA) of primate BRCA1 DNA
## repair genes
data("brca1_aln2", package = "GenomAutomorphism")
brca1_aln2
#> DNAMultipleAlignment with 41 rows and 2283 columns
#> aln names
#> [1] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [2] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA U64805.1:1-2280_H...
#> [3] ATGGATTTCTCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [4] ATGGATTTGTCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [5] ATGGATTTTTCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [6] ATGGATTTTTCTGCTCTTCGGGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [7] ATGGATTTTTCTGCTCTTCGCTTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [8] ATGGATTTTTCTGCTCTTCGCCTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [9] ATGGATTTTTCTGCTCTTCGCATTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> ... ...
#> [33] ATGGATTTATCTGCTCTTCGCGTTG...TCAGATCCCCCACAGCCACTACTGA XM_034941185.1:24...
#> [34] ATGGATTTATCTGCTCTTCGCGTTG...TCAGATCCCCCACAGCCACTACTGA XM_034941182.1:25...
#> [35] ATGGATTTATCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_032163757.1:14...
#> [36] ATGGATTTATCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_032163756.1:14...
#> [37] ATGGATTTATCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_032163758.1:13...
#> [38] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_030923119.1:18...
#> [39] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_030923118.1:18...
#> [40] ATGGATTTACCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_025363316.1:14...
#> [41] ATGGATTTATCTGCTGTTCGTGTTG...CCAGATCCCTCACAGCCACTACTGA XM_039475995.1:49...
## Get BaseSeq-class object
gr <- seq2granges(brca1_aln2)
gr
#> BaseSeq object with 2283 ranges and 41 metadata columns:
#> seqnames ranges strand | S1 S2 S3
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] 1 1 + | A A A
#> [2] 1 2 + | T T T
#> [3] 1 3 + | G G G
#> [4] 1 4 + | G G G
#> [5] 1 5 + | A A A
#> ... ... ... ... . ... ... ...
#> [2279] 1 2279 + | A A A
#> [2280] 1 2280 + | C C C
#> [2281] 1 2281 + | T T T
#> [2282] 1 2282 + | G G G
#> [2283] 1 2283 + | A A A
#> S4 S5 S6 S7 S8
#> <character> <character> <character> <character> <character>
#> [1] A A A A A
#> [2] T T T T T
#> [3] G G G G G
#> [4] G G G G G
#> [5] A A A A A
#> ... ... ... ... ... ...
#> [2279] A A A A A
#> [2280] C C C C C
#> [2281] T T T T T
#> [2282] G G G G G
#> [2283] A A A A A
#> S9 S10 S11 S12 S13
#> <character> <character> <character> <character> <character>
#> [1] A A A A A
#> [2] T T T T T
#> [3] G G G G G
#> [4] G G G G G
#> [5] A A A A A
#> ... ... ... ... ... ...
#> [2279] A A A A A
#> [2280] C C C C C
#> [2281] T T T T T
#> [2282] G G G G G
#> [2283] A A A A A
#> S14 S15 S16 S17 S18
#> <character> <character> <character> <character> <character>
#> [1] A A A A A
#> [2] T T T T T
#> [3] G G G G G
#> [4] G G G G G
#> [5] A A A A A
#> ... ... ... ... ... ...
#> [2279] A A A A A
#> [2280] C C C C C
#> [2281] T T T T T
#> [2282] G G G G G
#> [2283] A A A A A
#> S19 S20 S21 S22 S23
#> <character> <character> <character> <character> <character>
#> [1] A A A A A
#> [2] T T T T T
#> [3] G G G G G
#> [4] G G G G G
#> [5] A A A A A
#> ... ... ... ... ... ...
#> [2279] A A A A A
#> [2280] C C C C C
#> [2281] T T T T T
#> [2282] G G G G G
#> [2283] A A A A A
#> S24 S25 S26 S27 S28
#> <character> <character> <character> <character> <character>
#> [1] A A A A A
#> [2] T T T T T
#> [3] G G G G G
#> [4] G G G G G
#> [5] A A A A A
#> ... ... ... ... ... ...
#> [2279] A A A A A
#> [2280] C C C C C
#> [2281] T T T T T
#> [2282] G G G G G
#> [2283] A A A A A
#> S29 S30 S31 S32 S33
#> <character> <character> <character> <character> <character>
#> [1] A A A A A
#> [2] T T T T T
#> [3] G G G G G
#> [4] G G G G G
#> [5] A A A A A
#> ... ... ... ... ... ...
#> [2279] A A A A A
#> [2280] C C C C C
#> [2281] T T T T T
#> [2282] G G G G G
#> [2283] A A A A A
#> S34 S35 S36 S37 S38
#> <character> <character> <character> <character> <character>
#> [1] A A A A A
#> [2] T T T T T
#> [3] G G G G G
#> [4] G G G G G
#> [5] A A A A A
#> ... ... ... ... ... ...
#> [2279] A A A A A
#> [2280] C C C C C
#> [2281] T T T T T
#> [2282] G G G G G
#> [2283] A A A A A
#> S39 S40 S41
#> <character> <character> <character>
#> [1] A A A
#> [2] T T T
#> [3] G G G
#> [4] G G G
#> [5] A A A
#> ... ... ... ...
#> [2279] A A A
#> [2280] C C C
#> [2281] T T T
#> [2282] G G G
#> [2283] A A A
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Transform the BaseSeq-class object into a DNAStringSet-class object
str_set <- base_seq2string_set(gr)
str_set
#> DNAStringSet object of length 41:
#> width seq names
#> [1] 2283 ATGGATTTATCTGCTCTTCGCGT...GATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [2] 2283 ATGGATTTATCTGCTCTTCGCGT...GATCCCCCACAGCCACTACTGA U64805.1:1-2280_H...
#> [3] 2283 ATGGATTTCTCTGCTCTTCGCGT...GATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [4] 2283 ATGGATTTGTCTGCTCTTCGCGT...GATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [5] 2283 ATGGATTTTTCTGCTCTTCGCGT...GATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> ... ... ...
#> [37] 2283 ATGGATTTATCTGCTGTTCGCGT...GATCCCCCACAGCCACTACTGA XM_032163758.1:13...
#> [38] 2283 ATGGATTTATCTGCTCTTCGCGT...GATCCCCCACAGCCACTACTGA XM_030923119.1:18...
#> [39] 2283 ATGGATTTATCTGCTCTTCGCGT...GATCCCCCACAGCCACTACTGA XM_030923118.1:18...
#> [40] 2283 ATGGATTTACCTGCTGTTCGCGT...GATCCCCCACAGCCACTACTGA XM_025363316.1:14...
#> [41] 2283 ATGGATTTATCTGCTGTTCGTGT...GATCCCTCACAGCCACTACTGA XM_039475995.1:49...
## Recovering the original MSA
DNAMultipleAlignment(as.character(str_set))
#> DNAMultipleAlignment with 41 rows and 2283 columns
#> aln names
#> [1] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [2] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA U64805.1:1-2280_H...
#> [3] ATGGATTTCTCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [4] ATGGATTTGTCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [5] ATGGATTTTTCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [6] ATGGATTTTTCTGCTCTTCGGGTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [7] ATGGATTTTTCTGCTCTTCGCTTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [8] ATGGATTTTTCTGCTCTTCGCCTTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> [9] ATGGATTTTTCTGCTCTTCGCATTG...CCAGATCCCCCACAGCCACTACTGA NM_007298.3:20-22...
#> ... ...
#> [33] ATGGATTTATCTGCTCTTCGCGTTG...TCAGATCCCCCACAGCCACTACTGA XM_034941185.1:24...
#> [34] ATGGATTTATCTGCTCTTCGCGTTG...TCAGATCCCCCACAGCCACTACTGA XM_034941182.1:25...
#> [35] ATGGATTTATCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_032163757.1:14...
#> [36] ATGGATTTATCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_032163756.1:14...
#> [37] ATGGATTTATCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_032163758.1:13...
#> [38] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_030923119.1:18...
#> [39] ATGGATTTATCTGCTCTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_030923118.1:18...
#> [40] ATGGATTTACCTGCTGTTCGCGTTG...CCAGATCCCCCACAGCCACTACTGA XM_025363316.1:14...
#> [41] ATGGATTTATCTGCTGTTCGTGTTG...CCAGATCCCTCACAGCCACTACTGA XM_039475995.1:49...
## Example 5.
base_matrix(base = aln, cube = "CGTA", group = "Z5")
#> BaseSeqMatrix object with 51 ranges and 2 metadata columns:
#> seqnames ranges strand | S1 S2
#> <Rle> <IRanges> <Rle> | <numeric> <numeric>
#> [1] 1 1 + | 4 4
#> [2] 1 2 + | 1 3
#> [3] 1 3 + | 1 1
#> [4] 1 4 + | 3 3
#> [5] 1 5 + | 4 4
#> ... ... ... ... . ... ...
#> [47] 1 47 + | 3 3
#> [48] 1 48 + | 4 1
#> [49] 1 49 + | 1 1
#> [50] 1 50 + | 4 3
#> [51] 1 51 + | 3 3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Example 5.