This is a AutomorphismList object carrying a list of pairwise
automorphisms between the SARS coronavirus GZ02 (GenBank: AY390556.1:
265-13398_13398-21485) and Bat SARS-like coronavirus isolate bat-SL-CoVZC45
(GenBank: MG772933.1:265-1345513455-21542), nonstructural_polyprotein. The
pairwise DNA sequence alignment is available in the dataset named
covid_aln and the automorphisms were estimated with function
aut3D.
Usage
data("autm_3d", package = "GenomAutomorphism")Format
AutomorphismList class object.
Examples
data("autm_3d", package = "GenomAutomorphism")
autm_3d
#> Automorphism object with 9722 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 + | GAG GAG E
#> [3] 1 3 + | AGC AGC S
#> [4] 1 4 + | CTT CTT L
#> [5] 1 5 + | GTT GTT V
#> ... ... ... ... . ... ... ...
#> [9718] 1 9718 + | TCA TCA S
#> [9719] 1 9719 + | ACT ACT T
#> [9720] 1 9720 + | CAG CAG Q
#> [9721] 1 9721 + | GCA GCA A
#> [9722] 1 9722 + | TAA TAA *
#> aa2 coord1 coord2 autm cube
#> <character> <matrix> <matrix> <character> <character>
#> [1] M 1:4:3 1:4:3 1,1,1 ACGT
#> [2] E 3:1:3 3:1:3 1,1,1 ACGT
#> [3] S 1:3:2 1:3:2 1,1,1 ACGT
#> [4] L 2:4:4 2:4:4 1,1,1 ACGT
#> [5] V 3:4:4 3:4:4 1,1,1 ACGT
#> ... ... ... ... ... ...
#> [9718] S 4:2:1 4:2:1 1,1,1 ACGT
#> [9719] T 1:2:4 1:2:4 1,1,1 ACGT
#> [9720] Q 2:1:3 2:1:3 1,1,1 ACGT
#> [9721] A 3:2:1 3:2:1 1,1,1 ACGT
#> [9722] * 4:1:1 4:1:1 1,1,1 ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths