The alphabets for the modifications used in this package are based on the compilation of DNA modifications https://dnamod.hoffmanlab.org by the Hoffman lab. The alphabet was modified to make it compatible for the Modstrings package.

If modifications are missing, let us know.

Table 1: List of supported DNA modifications by ModDNAString objects
modification short name nomenclature orig. base abbreviation
5-putrescinylthymine 5pT 5pT T p
3-methylthymine 3mT 3mT T δ
O4-methylthymine O4meT O4meT T O
1-methylthymine 1mT 1mT T ]
5,6-dihydrothymine dhT dhT T D
β-glucosyl-hydroxymethyluracil baseJ baseJ T J
5-formyluracil 5fU 5fU T e
5-hydroxymethyluracil 5hmU 5hmU T g
5-dihydroxypentyluracil dhpU dhpU T `
5-carboxyluracil 5caU 5caU T b
2’-deoxyuridine dU dU T U
5,6-dihydroxy-2’-deoxyuridine DHdU DHdU T ∝
5-(2-aminoethyl)uridine 5nmU 5nmU T π
2’-deoxyinosine dI dI A I
7-methylguanine 7mG 7mG G 7
6-O-methylguanine 6mG 6mG G 6
3-methylguanine 3mG 3mG G 3
2-methylguanine 2mG 2mG G 2
1-methylguanine 1mG 1mG G 1
8-oxoguanine 8oxoG 8oxoG G 8
7-amido-7-deazaguanosine 7a7dG 7a7dG G ∉
1,N2-ethenoguanine 12eG 12eG G ⊆
N2,3-ethenoguanine 23eG 23eG G ⊇
N2,N2-dimethylguanosine 2,2mG 2,2mG G R
N2-carboxyethylguanine 2ceG 2ceG G α
5-methylcytosine 5mC 5mC C m
5-hydroxymethylcytosine 5hmC 5hmC C h
5-glucosylmethylcytosine 5gmC 5gmC C ×
5-formylcytosine 5fC 5fC C f
5-carboxylcytosine 5caC 5caC C 4
4-methylcytosine 4mC 4mC C ν
3,N4-ethenocytosine 34eC 34eC C X
3-methylcytosine 3mC 3mC C ’
3-ethylcytosine 3eC 3eC C κ
2-O-methylcytosine 2mC 2mC C o
1-methylcytosine 1mC 1mC C (
9-methyladenine 9mA 9mA A )
7-methyladenine 7mA 7mA A η
6-methyladenine 6mA 6mA A a
4-methyladenine 4mA 4mA A ⇓
3-methyladenine 3mA 3mA A ⇑
1-methyladenine 1mA 1mA A “
6-hydroxyaminopurine 6haA 6haA A √
2-aminoadenine 2mA 2mA A /
2-amino-6-hydroxyaminopurine 2a6haA 2a6haA A ≡
N6,N6-dimethyladenine 6,6mA 6,6mA A ζ
N6-carbamoylmethyladenine 6ncmA 6ncmA A ~ 
sessioninfo::session_info()
## ─ Session info ────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.0 (2019-04-26)
##  os       Ubuntu 18.04.2 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  C                           
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2019-05-02                  
## 
## ─ Packages ────────────────────────────────────────────────────────────────
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##  assertive.code         0.0-3     2018-10-21 [2] CRAN (R 3.6.0)
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##  assertive.files        0.0-2     2016-05-10 [2] CRAN (R 3.6.0)
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##  assertive.models       0.0-2     2018-10-21 [2] CRAN (R 3.6.0)
##  assertive.numbers      0.0-2     2016-05-09 [2] CRAN (R 3.6.0)
##  assertive.properties   0.0-4     2016-12-30 [2] CRAN (R 3.6.0)
##  assertive.reflection   0.0-4     2016-12-30 [2] CRAN (R 3.6.0)
##  assertive.sets         0.0-3     2016-12-30 [2] CRAN (R 3.6.0)
##  assertive.strings      0.0-3     2016-05-10 [2] CRAN (R 3.6.0)
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##  assertthat             0.2.1     2019-03-21 [2] CRAN (R 3.6.0)
##  BiocGenerics         * 0.30.0    2019-05-02 [2] Bioconductor  
##  BiocManager            1.30.4    2018-11-13 [2] CRAN (R 3.6.0)
##  BiocStyle            * 2.12.0    2019-05-02 [2] Bioconductor  
##  Biostrings           * 2.52.0    2019-05-02 [2] Bioconductor  
##  bitops                 1.0-6     2013-08-17 [2] CRAN (R 3.6.0)
##  bookdown               0.9       2018-12-21 [2] CRAN (R 3.6.0)
##  cli                    1.1.0     2019-03-19 [2] CRAN (R 3.6.0)
##  codetools              0.2-16    2018-12-24 [2] CRAN (R 3.6.0)
##  crayon                 1.3.4     2017-09-16 [2] CRAN (R 3.6.0)
##  digest                 0.6.18    2018-10-10 [2] CRAN (R 3.6.0)
##  evaluate               0.13      2019-02-12 [2] CRAN (R 3.6.0)
##  GenomeInfoDb           1.20.0    2019-05-02 [2] Bioconductor  
##  GenomeInfoDbData       1.2.1     2019-04-26 [2] Bioconductor  
##  GenomicRanges          1.36.0    2019-05-02 [2] Bioconductor  
##  highr                  0.8       2019-03-20 [2] CRAN (R 3.6.0)
##  htmltools              0.3.6     2017-04-28 [2] CRAN (R 3.6.0)
##  IRanges              * 2.18.0    2019-05-02 [2] Bioconductor  
##  knitr                  1.22      2019-03-08 [2] CRAN (R 3.6.0)
##  magrittr               1.5       2014-11-22 [2] CRAN (R 3.6.0)
##  Modstrings           * 1.0.0     2019-05-02 [1] Bioconductor  
##  Rcpp                   1.0.1     2019-03-17 [2] CRAN (R 3.6.0)
##  RCurl                  1.95-4.12 2019-03-04 [2] CRAN (R 3.6.0)
##  rmarkdown              1.12      2019-03-14 [2] CRAN (R 3.6.0)
##  S4Vectors            * 0.22.0    2019-05-02 [2] Bioconductor  
##  sessioninfo            1.1.1     2018-11-05 [2] CRAN (R 3.6.0)
##  stringi                1.4.3     2019-03-12 [2] CRAN (R 3.6.0)
##  stringr                1.4.0     2019-02-10 [2] CRAN (R 3.6.0)
##  withr                  2.1.2     2018-03-15 [2] CRAN (R 3.6.0)
##  xfun                   0.6       2019-04-02 [2] CRAN (R 3.6.0)
##  XVector              * 0.24.0    2019-05-02 [2] Bioconductor  
##  yaml                   2.2.0     2018-07-25 [2] CRAN (R 3.6.0)
##  zlibbioc               1.30.0    2019-05-02 [2] Bioconductor  
## 
## [1] /tmp/Rtmp3LPZGE/Rinst261282ababc
## [2] /home/biocbuild/bbs-3.9-bioc/R/library