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Automorphisms between DNA Sequences from Primate BRCA1 Genes

Source: R/data_brca1_autm.R
brca1_autm.Rd

This is a AutomorphismList object carrying a list of pairwise automorphisms between the DNA sequences from the MSA of primate BRCA1 DNA repair gene. The automorphisms were estimated from the brca1_aln MSA with function autZ64.

Usage

data("brca1_autm", package = "GenomAutomorphism")

Format

AutomorphismList class object.

See also

brca1_autm2, brca1_aln, brca1_aln2, and covid_autm.

Author

Robersy Sanchez https://genomaths.com

Examples

data("brca1_autm", package = "GenomAutomorphism")
brca1_autm
#> AutomorphismList object of length: 190
#> names(190): human_1.human_2 human_1.gorilla_1 human_1.gorilla_2 ... golden_monkey_2.gelada_baboon golden_monkey_2.bolivian_monkey gelada_baboon.bolivian_monkey 
#> ------- 
#> Automorphism object with 761 ranges and 8 metadata columns:
#>         seqnames    ranges strand |        seq1        seq2         aa1
#>            <Rle> <IRanges>  <Rle> | <character> <character> <character>
#>     [1]        1         1      + |         ATG         ATG           M
#>     [2]        1         2      + |         GAT         GAT           D
#>     [3]        1         3      + |         TTA         TTA           L
#>     [4]        1         4      + |         TCT         TCT           S
#>     [5]        1         5      + |         GCT         GCT           A
#>     ...      ...       ...    ... .         ...         ...         ...
#>   [757]        1       757      + |         CAC         CAC           H
#>   [758]        1       758      + |         AGC         AGC           S
#>   [759]        1       759      + |         CAC         CAC           H
#>   [760]        1       760      + |         TAC         TAC           Y
#>   [761]        1       761      + |         TGA         TGA           *
#>                 aa2    coord1    coord2      autm        cube
#>         <character> <numeric> <numeric> <numeric> <character>
#>     [1]           M        50        50         1        ACGT
#>     [2]           D        11        11         1        ACGT
#>     [3]           L        60        60         1        ACGT
#>     [4]           S        31        31         1        ACGT
#>     [5]           A        27        27         1        ACGT
#>     ...         ...       ...       ...       ...         ...
#>   [757]           H         5         5         1        ACGT
#>   [758]           S        33        33         1        ACGT
#>   [759]           H         5         5         1        ACGT
#>   [760]           Y        13        13         1        ACGT
#>   [761]           *        44        44         1        ACGT
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> ...
#> <189 more DFrame element(s)>
#> Two slots: 'DataList' & 'SeqRanges'
#> -------