Details on the DNA modification alphabet used by the Modstrings package
Modstrings 1.23.0
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 | ~ |
sessionInfo()## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB 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: America/New_York
## 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_1.43.0
## [4] XVector_0.47.0 IRanges_2.41.0 S4Vectors_0.45.0
## [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_1.3.0 jsonlite_1.8.9
## [10] glue_1.8.0 htmltools_0.5.8.1 sass_0.4.9
## [13] rmarkdown_2.28 evaluate_1.0.1 jquerylib_0.1.4
## [16] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
## [19] bookdown_0.41 stringr_1.5.1 BiocManager_1.30.25
## [22] compiler_4.5.0 digest_0.6.37 R6_2.5.1
## [25] GenomeInfoDbData_1.2.13 magrittr_2.0.3 GenomicRanges_1.59.0
## [28] bslib_0.8.0 tools_4.5.0 zlibbioc_1.53.0
## [31] cachem_1.1.0