ModDNAString alphabet

Felix G.M. Ernst & Denis L.J. Lafontaine

2024-03-26

Source: vignettes/ModDNAString-alphabet.Rmd

Abstract

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, Viner, and Hoffman 2019). The alphabet was modified to make it compatible for the Modstrings package.

If modifications are missing, let us know.

List of DNA modifications supported 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 ~ 
## R Under development (unstable) (2024-03-24 r86185)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 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-r0.3.20.so;  LAPACK version 3.10.0
## 
## 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_1.19.0   Biostrings_2.71.5   GenomeInfoDb_1.39.9
## [4] XVector_0.43.1      IRanges_2.37.1      S4Vectors_0.41.5   
## [7] BiocGenerics_0.49.1 BiocStyle_2.31.0   
## 
## loaded via a namespace (and not attached):
##  [1] jsonlite_1.8.8          compiler_4.4.0          BiocManager_1.30.22    
##  [4] crayon_1.5.2            stringr_1.5.1           GenomicRanges_1.55.4   
##  [7] jquerylib_0.1.4         systemfonts_1.0.6       textshaping_0.3.7      
## [10] yaml_2.3.8              fastmap_1.1.1           R6_2.5.1               
## [13] knitr_1.45              bookdown_0.38           desc_1.4.3             
## [16] GenomeInfoDbData_1.2.11 bslib_0.6.2             rlang_1.1.3            
## [19] stringi_1.8.3           cachem_1.0.8            xfun_0.43              
## [22] fs_1.6.3                sass_0.4.9              memoise_2.0.1          
## [25] cli_3.6.2               pkgdown_2.0.7           magrittr_2.0.3         
## [28] zlibbioc_1.49.3         digest_0.6.35           lifecycle_1.0.4        
## [31] vctrs_0.6.5             glue_1.7.0              evaluate_0.23          
## [34] ragg_1.3.0              rmarkdown_2.26          purrr_1.0.2            
## [37] tools_4.4.0             htmltools_0.5.8

References

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.