References

The alphabets for the modifications used in this package are based on the compilation of RNA modifications by the Bujnicki lab (Boccaletto et al. 2018). The alphabet was modified to remove some incompatible characters.

If modifications are missing, let us know.

Table 1: List of supported RNA modifications by ModRNAString objects
modification	short name	nomenclature	orig. base	abbreviation
1,2’-O-dimethyladenosine	m1Am	01A	A	œ
1,2’-O-dimethylguanosine	m1Gm	01G	G	ε
1,2’-O-dimethylinosine	m1Im	019A	A	ξ
1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine	m1acp3Y	1309U	U	α
1-methyladenosine	m1A	1A	A	“
1-methylguanosine	m1G	1G	G	K
1-methylinosine	m1I	19A	A	O
1-methylpseudouridine	m1Y	19U	U	]
2,8-dimethyladenosine	m2,8A	28A	A	±
2-geranylthiouridine	ges2U	21U	U	Γ
2-lysidine	k2C	21C	C	}
2-methyladenosine	m2A	2A	A	/
2-methylthiomethylenethio-N6-isopentenyl-adenosine	msms2i6A	2361A	A	£
2-methylthio-cyclic-N6-threonylcarbamoyladenosine	ms2ct6A	2164A	A	ÿ
2-methylthio-N6-(cis-hydroxyisopentenyl)-adenosine	ms2io6A	2160A	A	≠
2-methylthio-N6-hydroxynorvalylcarbamoyladenosine	ms2hn6A	2163A	A	≈
2-methylthio-N6-isopentenyladenosine	ms2i6A	2161A	A	*
2-methylthio-N6-methyladenosine	ms2m6A	621A	A	∞
2-methylthio-N6-threonylcarbamoyladenosine	ms2t6A	2162A	A	[
2-selenouridine	se2U	20U	U	ω
2-thio-2’-O-methyluridine	s2Um	02U	U	∏
2-thiocytidine	s2C	2C	C	%
2-thiouridine	s2U	2U	U	2
2’-O-methyladenosine	Am	0A	A	:
2’-O-methylcytidine	Cm	0C	C	B
2’-O-methylguanosine	Gm	0G	G	#
2’-O-methylinosine	Im	09A	A	≤
2’-O-methylpseudouridine	Ym	09U	U	Z
2’-O-methyluridine	Um	0U	U	J
2’-O-methyluridine 5-oxyacetic acid methyl ester	mcmo5Um	0503U	U	Ä
2’-O-ribosyladenosine (phosphate)	Ar(p)	00A	A	^
2’-O-ribosylguanosine (phosphate)	Gr(p)	00G	G	ℑ
3,2’-O-dimethyluridine	m3Um	03U	U	σ
3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine	acp3D	308U	U	Ð
3-(3-amino-3-carboxypropyl)pseudouridine	acp3Y	309U	U	Þ
3-(3-amino-3-carboxypropyl)uridine	acp3U	30U	U	X
3-methylcytidine	m3C	3C	C	’
3-methylpseudouridine	m3Y	39U	U	κ
3-methyluridine	m3U	3U	U	δ
4-demethylwyosine	imG-14	4G	G	†
4-thiouridine	s4U	74U	U	4
5,2’-O-dimethylcytidine	m5Cm	05C	C	τ
5,2’-O-dimethyluridine	m5Um	05U	U	¤
5-(carboxyhydroxymethyl)-2’-O-methyluridine methyl ester	mchm5Um	0522U	U	b
5-(carboxyhydroxymethyl)uridine methyl ester	mchm5U	522U	U	,
5-(isopentenylaminomethyl)-2-thiouridine	inm5s2U	2583U	U	½
5-(isopentenylaminomethyl)-2’-O-methyluridine	inm5Um	0583U	U	¼
5-(isopentenylaminomethyl)uridine	inm5U	583U	U	¾
5-aminomethyl-2-geranylthiouridine	nm5ges2U	21510U	U	Δ
5-aminomethyl-2-selenouridine	nm5se2U	20510U	U	π
5-aminomethyl-2-thiouridine	nm5s2U	2510U	U	∫
5-aminomethyluridine	nm5U	510U	U	∪
5-carbamoylhydroxymethyluridine	nchm5U	531U	U	r
5-carbamoylmethyl-2-thiouridine	ncm5s2U	253U	U	l
5-carbamoylmethyl-2’-O-methyluridine	ncm5Um	053U	U	~
5-carbamoylmethyluridine	ncm5U	53U	U	&
5-carboxyhydroxymethyluridine	chm5U	520U	U	≥
5-carboxymethyl-2-thiouridine	cm5s2U	2540U	U	℘
5-carboxymethylaminomethyl-2-geranylthiouridine	cmnm5ges2U	2151U	U	f
5-carboxymethylaminomethyl-2-selenouridine	cmnm5se2U	2051U	U	⊥
5-carboxymethylaminomethyl-2-thiouridine	cmnm5s2U	251U	U	$
5-carboxymethylaminomethyl-2’-O-methyluridine	cmnm5Um	051U	U	)
5-carboxymethylaminomethyluridine	cmnm5U	51U	U	!
5-carboxymethyluridine	cm5U	52U	U	◊
5-cyanomethyluridine	cnm5U	55U	U	Ѷ
5-formyl-2’-O-methylcytidine	f5Cm	071C	C	°
5-formylcytidine	f5C	71C	C	×
5-hydroxycytidine	ho5C	50C	C	Ç
5-hydroxymethylcytidine	hm5C	51C	C	∅
5-hydroxyuridine	ho5U	50U	U	∝
5-methoxycarbonylmethyl-2-thiouridine	mcm5s2U	2521U	U	3
5-methoxycarbonylmethyl-2’-O-methyluridine	mcm5Um	0521U	U	∩
5-methoxycarbonylmethyluridine	mcm5U	521U	U	1
5-methoxyuridine	mo5U	501U	U	5
5-methyl-2-thiouridine	m5s2U	25U	U	F
5-methylaminomethyl-2-geranylthiouridine	mnm5ges2U	21511U	U	h
5-methylaminomethyl-2-selenouridine	mnm5se2U	20511U	U	≅
5-methylaminomethyl-2-thiouridine	mnm5s2U	2511U	U	S
5-methylaminomethyluridine	mnm5U	511U	U	{
5-methylcytidine	m5C	5C	C	?
5-methyldihydrouridine	m5D	58U	U	ρ
5-methyluridine	m5U	5U	U	T
5-taurinomethyl-2-thiouridine	tm5s2U	254U	U	∃
5-taurinomethyluridine	tm5U	54U	U	Ê
7-aminocarboxypropyl-demethylwyosine	yW-86	47G	G	¥
7-aminocarboxypropylwyosine	yW-72	347G	G	Ω
7-aminocarboxypropylwyosine methyl ester	yW-58	348G	G	⇑
7-aminomethyl-7-deazaguanosine	preQ1tRNA	101G	G	∉
7-cyano-7-deazaguanosine	preQ0tRNA	100G	G	φ
7-methylguanosine	m7G	7G	G	7
8-methyladenosine	m8A	8A	A	â
N2,2’-O-dimethylguanosine	m2Gm	02G	G	γ
N2,7,2’-O-trimethylguanosine	m2,7Gm	027G	G	æ
N2,7-dimethylguanosine	m2,7G	27G	G	∨
N2,N2,2’-O-trimethylguanosine	m2,2Gm	022G	G	\|
N2,N2,7-trimethylguanosine	m2,2,7G	227G	G	∠
N2,N2-dimethylguanosine	m2,2G	22G	G	R
N2-methylguanosine	m2G	2G	G	L
N4,2’-O-dimethylcytidine	m4Cm	04C	C	λ
N4,N4,2’-O-trimethylcytidine	m4,4Cm	044C	C	β
N4,N4-dimethylcytidine	m4,4C	44C	C	μ
N4-acetyl-2’-O-methylcytidine	ac4Cm	042C	C	ℵ
N4-acetylcytidine	ac4C	42C	C	M
N4-methylcytidine	m4C	4C	C	ν
N6,2’-O-dimethyladenosine	m6Am	06A	A	χ
N6,N6,2’-O-trimethyladenosine	m6,6Am	066A	A	η
N6,N6-dimethyladenosine	m6,6A	66A	A	ζ
N6-(cis-hydroxyisopentenyl)adenosine	io6A	60A	A	`
N6-acetyladenosine	ac6A	64A	A	⇓
N6-formyladenosine	f6A	67A	A	Ϩ
N6-glycinylcarbamoyladenosine	g6A	65A	A	≡
N6-hydroxymethyladenosine	hm6A	68A	A	Ϫ
N6-hydroxynorvalylcarbamoyladenosine	hn6A	63A	A	√
N6-isopentenyladenosine	i6A	61A	A	Θ
N6-methyl-N6-threonylcarbamoyladenosine	m6t6A	662A	A	E
N6-methyladenosine	m6A	6A	A	=
N6-threonylcarbamoyladenosine	t6A	62A	A	6
agmatidine	C+	20C	C	¿
archaeosine	G+	103G	G	(
cyclic N6-threonylcarbamoyladenosine	ct6A	69A	A	e
dihydrouridine	D	8U	U	D
epoxyqueuosine	oQtRNA	102G	G	ς
galactosyl-queuosine	galQtRNA	104G	G	9
glutamyl-queuosine	gluQtRNA	105G	G	⊄
hydroxy-N6-threonylcarbamoyladenosine	ht6A	2165A	A	«
hydroxywybutosine	OHyW	34830G	G	⊆
inosine	I	9A	A	I
isowyosine	imG2	42G	G	⊇
mannosyl-queuosine	manQtRNA	106G	G	8
methylated undermodified hydroxywybutosine	OHyWy	3480G	G	y
methylwyosine	mimG	342G	G	∑
peroxywybutosine	o2yW	34832G	G	W
pseudouridine	Y	9U	U	P
queuosine	QtRNA	10G	G	Q
undermodified hydroxywybutosine	OHyWx	3470G	G	š
unknown methylated base	Xm	0X	N	Î
unknown modification	xX	X	N	÷
unknown modified adenosine	xA	?A	A	H
unknown modified cytidine	xC	?C	C	<
unknown modified guanosine	xG	?G	G	;
unknown modified uridine	xU	?U	U	Ü
uridine 5-oxyacetic acid	cmo5U	502U	U	V
uridine 5-oxyacetic acid methyl ester	mcmo5U	503U	U	υ
wybutosine	yW	3483G	G	Y
wyosine	imG	34G	G	€

sessionInfo()

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.9-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.9-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
## [1] Modstrings_1.0.3    Biostrings_2.52.0   XVector_0.24.0     
## [4] IRanges_2.18.1      S4Vectors_0.22.0    BiocGenerics_0.30.0
## [7] BiocStyle_2.12.0   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.1                 assertive.data_0.0-3      
##  [3] highr_0.8                  compiler_3.6.0            
##  [5] BiocManager_1.30.4         GenomeInfoDb_1.20.0       
##  [7] bitops_1.0-6               assertive.files_0.0-2     
##  [9] tools_3.6.0                assertive.properties_0.0-4
## [11] zlibbioc_1.30.0            assertive.data.us_0.0-2   
## [13] digest_0.6.19              assertive_0.3-5           
## [15] evaluate_0.14              assertive.base_0.0-7      
## [17] yaml_2.2.0                 xfun_0.8                  
## [19] GenomeInfoDbData_1.2.1     stringr_1.4.0             
## [21] knitr_1.23                 assertive.sets_0.0-3      
## [23] assertive.matrices_0.0-2   assertive.strings_0.0-3   
## [25] assertive.types_0.0-3      assertive.datetimes_0.0-2 
## [27] assertive.code_0.0-3       rmarkdown_1.13            
## [29] bookdown_0.11              magrittr_1.5              
## [31] assertive.models_0.0-2     assertive.numbers_0.0-2   
## [33] codetools_0.2-16           htmltools_0.3.6           
## [35] GenomicRanges_1.36.0       stringi_1.4.3             
## [37] assertive.data.uk_0.0-2    RCurl_1.95-4.12           
## [39] assertive.reflection_0.0-4

References

Boccaletto, Pietro, Magdalena A. Machnicka, Elzbieta Purta, Pawel Piatkowski, Blazej Baginski, Tomasz K. Wirecki, Valérie de Crécy-Lagard, et al. 2018. “MODOMICS: A Database of Rna Modification Pathways. 2017 Update.” Nucleic Acids Research 46 (D1):D303–D307. https://doi.org/10.1093/nar/gkx1030.

ModRNAString alphabet

2019-06-25

Abstract

Package

Contents

References