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 autZ64.
Usage
data("autm", package = "GenomAutomorphism")Format
AutomorphismList class object.
Details
The alignment of these DNA sequences is available at: https://github.com/genomaths/seqalignments/raw/master/COVID-19 in the fasta file 'AY390556.1_265-13398_13398-21485_RNA-POL_SARS_COVI_GZ02.fas'
Examples
data("autm", package = "GenomAutomorphism")
autm
#> Automorphism object with 7100 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 GTC V
#> ... ... ... ... . ... ... ...
#> [7096] 1 7096 + | CTT CTT L
#> [7097] 1 7097 + | GTT GTT V
#> [7098] 1 7098 + | AAT AAC N
#> [7099] 1 7099 + | AAC AAC N
#> [7100] 1 7100 + | TAA TAA *
#> aa2 coord1 coord2 autm cube
#> <character> <numeric> <numeric> <numeric> <character>
#> [1] M 50 50 1 ACGT
#> [2] E 10 10 1 ACGT
#> [3] S 33 33 1 ACGT
#> [4] L 55 55 1 ACGT
#> [5] V 59 57 27 ACGT
#> ... ... ... ... ... ...
#> [7096] L 55 55 1 ACGT
#> [7097] V 59 59 1 ACGT
#> [7098] N 3 1 43 ACGT
#> [7099] N 1 1 1 ACGT
#> [7100] * 12 12 1 ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths