Details on the DNA modification alphabet used by the Modstrings package
Modstrings 1.16.0
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 version 4.3.0 RC (2023-04-13 r84269 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server 2022 x64 (build 20348)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Modstrings_1.16.0 Biostrings_2.68.0 GenomeInfoDb_1.36.0
## [4] XVector_0.40.0 IRanges_2.34.0 S4Vectors_0.38.0
## [7] BiocGenerics_0.46.0 BiocStyle_2.28.0
##
## loaded via a namespace (and not attached):
## [1] crayon_1.5.2 cli_3.6.1 knitr_1.42
## [4] rlang_1.1.0 xfun_0.39 stringi_1.7.12
## [7] jsonlite_1.8.4 glue_1.6.2 RCurl_1.98-1.12
## [10] htmltools_0.5.5 sass_0.4.5 rmarkdown_2.21
## [13] evaluate_0.20 jquerylib_0.1.4 bitops_1.0-7
## [16] fastmap_1.1.1 lifecycle_1.0.3 yaml_2.3.7
## [19] bookdown_0.33 stringr_1.5.0 BiocManager_1.30.20
## [22] compiler_4.3.0 digest_0.6.31 R6_2.5.1
## [25] GenomeInfoDbData_1.2.10 magrittr_2.0.3 GenomicRanges_1.52.0
## [28] bslib_0.4.2 tools_4.3.0 zlibbioc_1.46.0
## [31] cachem_1.0.7
Sood, Ankur Jai, Coby Viner, and Michael M. Hoffman. 2019. “DNAmod: The Dna Modification Database.” Journal of Cheminformatics 11 (1): 30. https://doi.org/10.1186/s13321-019-0349-4.