vignettes/ModDNAString-alphabet.Rmd
ModDNAString-alphabet.RmdAbstract
Details on the DNA modification alphabet used by the Modstrings package
The alphabets for the modifications used in this package are based on
the compilation of DNA modifications by the Hoffman lab (Sood et al. 2019). The alphabet was modified to
make it compatible for the Modstrings package.
If modifications are missing, let us know.
| 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 | ~ |
## R version 4.5.1 (2025-06-13)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Modstrings_1.25.0 Biostrings_2.77.2 Seqinfo_0.99.2
## [4] XVector_0.49.1 IRanges_2.43.2 S4Vectors_0.47.2
## [7] BiocGenerics_0.55.1 generics_0.1.4 BiocStyle_2.37.1
##
## loaded via a namespace (and not attached):
## [1] crayon_1.5.3 cli_3.6.5 knitr_1.50
## [4] rlang_1.1.6 xfun_0.53 stringi_1.8.7
## [7] textshaping_1.0.3 jsonlite_2.0.0 glue_1.8.0
## [10] htmltools_0.5.8.1 ragg_1.5.0 sass_0.4.10
## [13] rmarkdown_2.29 evaluate_1.0.5 jquerylib_0.1.4
## [16] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
## [19] bookdown_0.44 stringr_1.5.2 BiocManager_1.30.26
## [22] compiler_4.5.1 fs_1.6.6 htmlwidgets_1.6.4
## [25] systemfonts_1.2.3 digest_0.6.37 R6_2.6.1
## [28] magrittr_2.0.4 GenomicRanges_1.61.4 bslib_0.9.0
## [31] tools_4.5.1 pkgdown_2.1.3 cachem_1.1.0
## [34] desc_1.4.3