HPV genome
Erqiang Hu: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University.
Shanye Yin： Albert Einstein College of Medicine
devtools::install_github("huerqiang/BSgenomehpv")This is a basic example which shows you how to solve a common problem:
library(BSgenomehpv)seqnames(BSgenomehpv)
#> [1] "M12732.1" "M12732.1_E6" "M12732.1_E7"
#> [4] "M12732.1_E1" "M12732.1_E2" "M12732.1_E4"
#> [7] "M12732.1_gene_6" "M12732.1_gene_7" "M12732.1_L1"
#> [10] "MT218010.1" "MT218010.1_E6" "MT218010.1_E7"
#> [13] "MT218010.1_E1" "MT218010.1_E2" "MT218010.1_E4"
#> [16] "MT218010.1_E5" "MT218010.1_L2" "MT218010.1_L1"
#> [19] "NC_001357.1" "NC_001357.1_E6" "NC_001357.1_E7"
#> [22] "NC_001357.1_E1" "NC_001357.1_E2" "NC_001357.1_E4"
#> [25] "NC_001357.1_E5" "NC_001357.1_L2" "NC_001357.1_L1"
#> [28] "NC_001526.1" "NC_001526.1_E6" "NC_001526.1_E7"
#> [31] "NC_001526.1_E1" "NC_001526.1_E2" "NC_001526.1_E4"
#> [34] "NC_001526.1_E5" "NC_001526.1_L2" "NC_001526.1_L1"
#> [37] "NC_001526.2" "NC_001526.2_E6" "NC_001526.2_E7"
#> [40] "NC_001526.2_E1" "NC_001526.2_E2" "NC_001526.2_E4"
#> [43] "NC_001526.2_E5" "NC_001526.2_L2" "NC_001526.2_L1"
#> [46] "NC_001526.3" "NC_001526.3_E6" "NC_001526.3_E7"
#> [49] "NC_001526.3_E1^E4" "NC_001526.3_E1" "NC_001526.3_E2"
#> [52] "NC_001526.3_E4" "NC_001526.3_E5" "NC_001526.3_L2"
#> [55] "NC_001526.3_L1" "NC_001526.4" "NC_001526.4_E1^E4"
#> [58] "NC_001526.4_E1" "NC_001526.4_E2" "NC_001526.4_E5"
#> [61] "NC_001526.4_L2" "NC_001526.4_L1" "NC_001526.4_E6"
#> [64] "NC_001526.4_E7"
getSeq(BSgenomehpv, "MT218010.1_E5", start = 10, end = 20)
#> 11-letter DNAString object
#> seq: CTTACAGCTTC
getSeq(BSgenomehpv, "NC_001526.2", start = 4570, end = 4667)
#> 98-letter DNAString object
#> seq: CTAGTTTTATTGATGCTGGTGCACCAACATCTGTAC...TTTAGTATTACTACTTCAACTGATACCACACCTGCT
## basic example code