The alphabets for the modifications used in this package are based on
the compilation of DNA modifications by the Hoffman lab (Sood, Viner, and Hoffman 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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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=C
## [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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Modstrings_1.23.0 Biostrings_2.75.0 GenomeInfoDb_1.41.2
## [4] XVector_0.45.0 IRanges_2.39.2 S4Vectors_0.43.2
## [7] BiocGenerics_0.53.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] crayon_1.5.3 httr_1.4.7 cli_3.6.3
## [4] knitr_1.48 rlang_1.1.4 xfun_0.48
## [7] stringi_1.8.4 UCSC.utils_1.1.0 jsonlite_1.8.9
## [10] glue_1.8.0 buildtools_1.0.0 htmltools_0.5.8.1
## [13] maketools_1.3.1 sys_3.4.3 sass_0.4.9
## [16] rmarkdown_2.28 evaluate_1.0.1 jquerylib_0.1.4
## [19] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
## [22] stringr_1.5.1 BiocManager_1.30.25 compiler_4.4.1
## [25] digest_0.6.37 R6_2.5.1 GenomeInfoDbData_1.2.13
## [28] magrittr_2.0.3 GenomicRanges_1.57.2 bslib_0.8.0
## [31] tools_4.4.1 zlibbioc_1.51.2 cachem_1.1.0