miRBaseConverter is an R/Bioconductor package for converting and retrieving the definition of miRNAs ( Names, Accessions, Sequences, Families and others) in different miRBase versions ( From miRBase version 6 to version 21 [ The latest version ] ). A tiny built-in database is embedded in the miRBaseConverter R package for retrieving miRNA information efficiently.
microRNAs( miRNAs) are one of the essential molecules that play the important role in the post-transcriptional gene regulation. The studies about novel miRNA and their function discoveries have an explosive growth in the last decade. The miRBase database is the authority archive of miRNA annotations and sequences for all species. With the development of researches about miRNAs, the annotation of miRNA has been changed significantly and develops many different historical versions. Each of the previous versions has been adopted in many research literatures and databases. Due to the inconsistent of name annotation of miRNAs, there is a barrier for the later scholars to reuse the previous research results in a convenient way, especially for miRNA databases with thousands of entries. There are some webservers or R-based tools can handle the batch conversion of miRNA names. However, an easy-to-use and well-documented tool for miRNA conversion and information retrieval is still lack. We present the miRBaseConverter R package, a comprehensive tool for miRNA research, to provide a suite of tools for checking miRNA Name, Accession, Sequence, version and family and history information. The miRBaseConverter package can be competent for all species including Precursor and Mature miRNAs defined in miRBase.
In addtion, we also develop an online application with interactive interface for this package which can be accessed in https://taoshengxu.shinyapps.io/miRBaseConverter/.
In the following sections, we present the detail usage of the functions included in the miRBaseConverter package.
For a list of miRNA names without version information, users may need to check what is the most possible miRBase version. miRBaseConverter package provides an easy-to-use function checkMiRNAVersion() to address this issue with an straightforward result.
library(miRBaseConverter)
data(miRNATest)
miRNANames = miRNATest$miRNA_Name
version=checkMiRNAVersion(miRNANames, verbose = TRUE)
## Version Proportion Recommend
## 1 v6 12.33%
## 2 v7_1 18.67%
## 3 v8 18.83%
## 4 v8_1 20.33%
## 5 v8_2 20.5%
## 6 v9 22%
## 7 v9_1 26%
## 8 v9_2 26%
## 9 v10 29%
## 10 v10_1 29.5%
## 11 v11 32.5%
## 12 v12 34%
## 13 v13 35.33%
## 14 v14 45.5%
## 15 v15 51.67%
## 16 v16 51.67%
## 17 v17 51.83%
## 18 v18 98.67% ***BEST Matched***
## 19 v19 90.83%
## 20 v20 82.83%
## 21 v21 78.5%The output text in console shows the matched proportions in all the miRBase version and gives the recommended version which is the best matched with the highest proportion values. This function is of great helpful miRNA version checking of a chunk of miRNAs.
An Accession is the identifier that define miRNA uniquely in miRBase. Users can apply Accessions to retrieve the entire information of the miRNAs in miRBase. One of the most commonly used functions is to retrieve the corresponding miRNA name from Accession. The manual retrieval one by one in miRBase could be a tough work for a chunk of Accessions of interest. The function miRNA_AccessionToName() in miRBaseConverter package can conduct a high throughput transformation within quite short time.
library(miRBaseConverter)
data(miRNATest)
Accessions = miRNATest$Accession
#### 1. Convert to the Accessions to miRNA names in miRBase version 13
result1 = miRNA_AccessionToName(Accessions,targetVersion = "v13")
result1[c(341:345),]
## Accession TargetName
## 341 MIMAT0002843 hsa-miR-520b
## 342 MIMAT0001650 mtr-miR399c
## 343 MIMAT0000013 cel-miR-42
## 344 MIMAT0002885 osa-miR529a
## 345 MIMAT0011111 <NA>
####2. Convert to the Accessions to miRNA names in miRBase version 21.
result2 = miRNA_AccessionToName(Accessions,targetVersion = "v21")
result2[c(341:345),]
## Accession TargetName
## 341 MIMAT0002843 hsa-miR-520b
## 342 MIMAT0001650 mtr-miR399c
## 343 MIMAT0000013 cel-miR-42-3p
## 344 MIMAT0002885 osa-miR529a
## 345 MIMAT0011111 mtr-miR169bThe conversion of miRNA Name to Accession is the reversion process. Due to the frequent changes of miRNA name in different versions, researches are likely to adopt the miRBase Accessions as the identifiers in most literatures and databases.
library(miRBaseConverter)
data(miRNATest)
miRNANames = miRNATest$miRNA_Name
result1 = miRNA_NameToAccession(miRNANames,version = "v18")
result1[c(341:345),]
## miRNAName_v18 Accession
## 341 hsa-miR-520b MIMAT0002843
## 342 mtr-miR399c MIMAT0001650
## 343 cel-miR-42-3p MIMAT0000013
## 344 osa-miR529a MIMAT0002885
## 345 mtr-miR169j MIMAT0011111In miRBaseConverter package, there are two ways to conduct the conversion of miRNA Names between two different miRBase versions.
miRBaseConverter package provides the miRNAVersionConvert() function to detect all the match miRNA Names with the same Accession in all miRBase historical versions. The conversion result may not match to the unique Name for some miRNAs but it is useful for all possible information retrieval for the miRNAs of interest.
library(miRBaseConverter)
data(miRNATest)
miRNANames = miRNATest$miRNA_Name
result1 = miRNAVersionConvert(miRNANames,targetVersion = "v13",exact = TRUE)
## ********************************************
## The multiple matched miRNAs are list below:
## original Version v13 Accession
## 1 hsa-let-7c hsa-let-7c&hsa-let-7c MI0000064&MIMAT0000064
## 2 cel-lsy-6 cel-lsy-6&cel-lsy-6 MI0000801&MIMAT0000749
result1[c(341:345),]
## OriginalName TargetName Accession
## 341 hsa-miR-520b hsa-miR-520b MIMAT0002843
## 342 mtr-miR399c mtr-miR399c MIMAT0001650
## 343 cel-miR-42-3p cel-miR-42 MIMAT0000013
## 344 osa-miR529a osa-miR529a MIMAT0002885
## 345 mtr-miR169j <NA> <NA>
result2 = miRNAVersionConvert(miRNANames,targetVersion = "v20",exact = TRUE)
## ********************************************
##
## The multiple matched miRNAs are list below:
## original Version v20 Accession
## 1 cel-lsy-6 cel-lsy-6&cel-lsy-6 MI0000801&MIMAT0000749
result2[c(341:345),]
## OriginalName TargetName Accession
## 341 hsa-miR-520b hsa-miR-520b MIMAT0002843
## 342 mtr-miR399c mtr-miR399c MIMAT0001650
## 343 cel-miR-42-3p cel-miR-42-3p MIMAT0000013
## 344 osa-miR529a osa-miR529a MIMAT0002885
## 345 mtr-miR169j mtr-miR169j MIMAT0013321The miRBase Accession can be a bridge to exactly match miRNA Name between two different miRBase versions. For a group of miRNA Names, users could apply the function checkMiRNAVersion() to check the possible miRNA version firstly. Then the miRNA Names accompanying with the version information are mapped to the Accessions using the function miRNA_NameToAccession(). In the last step, the Accessions can be easily mapped to the miRNA Names in the target version. This approach can output more exact result than the global searching and matching.
[ checkMiRNAVersion()-> miRNA_NameToAccession() -> miRNA_AccessionToName() ]
library(miRBaseConverter)
data(miRNATest)
miRNANames = miRNATest$miRNA_Name
#### Step 1. Check the possible version for miRNAs
data(miRNATest)
miRNANames = miRNATest$miRNA_Name
version=checkMiRNAVersion(miRNANames, verbose = FALSE)
#### Step 2. miRNA Names to miRBase Accessions with the specific version information
result1 = miRNA_NameToAccession(miRNANames,version = version)
#### Step 3. miRBase Accessions to miRNA Names of the target version
result2 = miRNA_AccessionToName(result1[,2],targetVersion = "v21")
result2[c(341:345),]
## Accession TargetName
## 341 MIMAT0002843 hsa-miR-520b
## 342 MIMAT0001650 mtr-miR399c
## 343 MIMAT0000013 cel-miR-42-3p
## 344 MIMAT0002885 osa-miR529a
## 345 MIMAT0011111 mtr-miR169bA Precursor miRNA is about 70mer RNA with a stem-loop to form as a hairpin structure. The 5’ UTR and/or 3’ UTR of the stem-loop can be cleaved by dicer to generate one or two mature miRNAs ( about 22 nucleotides ). In miRBaseConverter package, we provide the functions for conversion between precursors and mature miRNAs.
library(miRBaseConverter)
data(miRNATest)
miRNANames=miRNATest$miRNA_Name
result1=miRNA_MatureToPrecursor(miRNANames)
## The input miRNA version information: miRBase v18
head(result1)
## OriginalName Precursor
## 1 cel-miR-46-3p cel-mir-46
## 2 cel-miR-81-3p cel-mir-81
## 3 cel-miR-1817 cel-mir-1817
## 4 hsa-miR-196a-5p hsa-mir-196a-1
## 5 mmu-miR-149-5p mmu-mir-149
## 6 mtr-miR166d mtr-MIR166dlibrary(miRBaseConverter)
miRNANames=c("pma-mir-100a","sko-mir-92a","hsa-mir-6131","mtr-MIR2655i",
"mmu-mir-153","mtr-MIR2592am","mml-mir-1239","xtr-mir-128-2","oan-mir-100",
"mmu-mir-378b","hsa-miR-508-5p","mmu-miR-434-3p")
result2=miRNA_PrecursorToMature(miRNANames)
## The input miRNA version information: miRBase v21
head(result2)
## OriginalName Mature1 Mature2
## 1 pma-mir-100a pma-miR-100a-5p pma-miR-100a-3p
## 2 sko-mir-92a sko-miR-92a <NA>
## 3 hsa-mir-6131 hsa-miR-6131 <NA>
## 4 mtr-MIR2655i mtr-miR2655i <NA>
## 5 mmu-mir-153 mmu-miR-153-5p mmu-miR-153-3p
## 6 mtr-MIR2592am mtr-miR2592am <NA>miRNAs are manually classified by the single-linkage method to cluster the precursor sequences based on BLAST hits and adjusted manually the clustered families by multiple sequence alignment in miRBase. The family classification is based on a common ancestor for each family representing sequences. Normally, the miRNAs from the same family may possess similar physiological functions in cell metabolism. In miRBaseConverter package, the function checkMiRNAFamliy() is specifically designed for the retrieval information of miRNA families. It can be applied to retrieve the miRNA families and family accessions for a list of miRNAs.
library(miRBaseConverter)
## The input is miRNA Accessions
Accessions=miRNATest$Accession
Family_Info1=checkMiRNAFamliy(Accessions)
head(Family_Info1)
## Accession miRNAName_v21 FamilyAccession Family
## 1 MIMAT0000017 cel-miR-46-3p MIPF0000087 mir-46
## 2 MIMAT0000054 cel-miR-81-3p MIPF0000154 mir-81
## 3 MIMAT0006584 cel-miR-1817 <NA> <NA>
## 4 MIMAT0000226 hsa-miR-196a-5p MIPF0000031 mir-196
## 5 MIMAT0000159 mmu-miR-149-5p MIPF0000274 mir-149
## 6 MIMAT0011068 mtr-miR166d MIPF0000004 MIR166
##The input is miRNA names
miRNANames=miRNATest$miRNA_Name
version=checkMiRNAVersion(miRNANames,verbose = FALSE)
result=miRNA_NameToAccession(miRNANames,version=version)
Accessions=result$Accession
Family_Info2=checkMiRNAFamliy(Accessions)
head(Family_Info2)
## Accession miRNAName_v21 FamilyAccession Family
## 1 MIMAT0000017 cel-miR-46-3p MIPF0000087 mir-46
## 2 MIMAT0000054 cel-miR-81-3p MIPF0000154 mir-81
## 3 MIMAT0006584 cel-miR-1817 <NA> <NA>
## 4 MIMAT0000226 hsa-miR-196a-5p MIPF0000031 mir-196
## 5 MIMAT0000159 mmu-miR-149-5p MIPF0000274 mir-149
## 6 MIMAT0011068 mtr-miR166d MIPF0000004 MIR166The miRNA sequence is great important for base alignment in the research of gene regulation. In miRBaseConverter package, we provide an efficient tool to batch retrieve the sequence of miRNAs based on the Accessions. It will be great help of automated analyses of sequence alignment between miRNAs and their target molecules.
library(miRBaseConverter)
data(miRNATest)
Accessions = miRNATest$Accession
result1 = getMiRNASequence(Accessions,targetVersion = "v13")
head(result1)
## Accession miRNASequence_v13
## 1 MIMAT0000017 UGUCAUGGAGUCGCUCUCUUCA
## 2 MIMAT0000054 UGAGAUCAUCGUGAAAGCUAGU
## 3 MIMAT0006584 UAGCCAAUGUCUUCUCUAUCAUG
## 4 MIMAT0000226 UAGGUAGUUUCAUGUUGUUGGG
## 5 MIMAT0000159 UCUGGCUCCGUGUCUUCACUCCC
## 6 MIMAT0011068 <NA>
result2 = getMiRNASequence(Accessions,targetVersion = "v21")
head(result2)
## Accession miRNASequence_v21
## 1 MIMAT0000017 UGUCAUGGAGUCGCUCUCUUCA
## 2 MIMAT0000054 UGAGAUCAUCGUGAAAGCUAGU
## 3 MIMAT0006584 UAGCCAAUGUCUUCUCUAUCAUG
## 4 MIMAT0000226 UAGGUAGUUUCAUGUUGUUGGG
## 5 MIMAT0000159 UCUGGCUCCGUGUCUUCACUCCC
## 6 MIMAT0011068 UCGGGCCAGGCUUCAUCCCCCCurrently, the latest miRBase version is 21 which was released in June 2014. In miRBaseConverter package, we implement a query function to check all the miRBase version information from miRBase version 1 to version 21. The return includes the information of the defined version names, release dates, the number of defined miRNAs (Entries including Precursors and Mature miRNAs) and the available status in miRBaseConverter package.
library(miRBaseConverter)
getAllVersionInfo()
## Version Date Entries Status
## 1 v1 12/2002 218 Unavailable
## 2 v1_1 01/2003 262 Unavailable
## 3 v1_2 04/2003 295 Unavailable
## 4 v1_3 05/2003 332 Unavailable
## 5 v1_4 07/2003 345 Unavailable
## 6 v2 07/2003 506 Unavailable
## 7 v2_1 09/2003 558 Unavailable
## 8 v2_2 11/2003 593 Unavailable
## 9 v3 01/2004 719 Unavailable
## 10 v3_1 04/2004 899 Unavailable
## 11 v4 07/2004 1185 Unavailable
## 12 v5 09/2004 1345 Unavailable
## 13 v5_1 12/2004 1420 Unavailable
## 14 v6 04/2005 1650 Available
## 15 v7 06/2005 2909 Unavailable
## 16 v7_1 10/2005 3424 Available
## 17 v8 02/2006 3518 Available
## 18 v8_1 05/2006 3963 Available
## 19 v8_2 07/2006 4039 Available
## 20 v9 10/2006 4361 Available
## 21 v9_1 02/2007 4449 Available
## 22 v9_2 05/2007 4584 Available
## 23 v10 08/2007 5071 Available
## 24 v10_1 12/2007 5395 Available
## 25 v11 04/2008 6396 Available
## 26 v12 09/2008 8619 Available
## 27 v13 03/2009 9539 Available
## 28 v14 09/2009 10883 Available
## 29 v15 04/2010 14197 Available
## 30 v16 08/2010 15172 Available
## 31 v17 04/2011 16772 Available
## 32 v18 11/2011 18226 Available
## 33 v19 08/2012 21264 Available
## 34 v20 06/2013 24521 Available
## 35 v21 06/2014 28645 AvailablemiRBase has defined the miRNAs for hundreds of species. In miRBaseConverter package, users can apply the function getAllSpecies() to check the abbreviation and the full name of the available species.
library(miRBaseConverter)
allSpecies=getAllSpecies()
head(allSpecies)
## Species FullName
## 1 aae Aedes aegypti
## 2 aau Acacia auriculiformis
## 3 aca Anolis carolinensis
## 4 aga Anopheles gambiae
## 5 age Ateles geoffroyi
## 6 ahy Arachis hypogaeaIn miRBaseConverter package, the function getAllMiRNAs() can be applied to get all miRNAs which are defined in each available miRBase version. Meanwhile, users can use the control parameters to custom the species and miRNA type in the output.
library(miRBaseConverter)
miRNAs=getAllMiRNAs(version="v21", type="all", species="hsa")
head(miRNAs)
## Accession Name Sequence
## 1 MI0000061 hsa-let-7a-2 AGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUUACAUCAAGGGAGAUAACUGUACAGCCUCCUAGCUUUCCU
## 2 MIMAT0010195 hsa-let-7a-2-3p CUGUACAGCCUCCUAGCUUUCC
## 3 MI0000062 hsa-let-7a-3 GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGGGAUAACUAUACAAUCUACUGUCUUUCCU
## 4 MIMAT0004481 hsa-let-7a-3p CUAUACAAUCUACUGUCUUUC
## 5 MIMAT0000062 hsa-let-7a-5p UGAGGUAGUAGGUUGUAUAGUU
## 6 MI0000063 hsa-let-7b CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCCCCUCGGAAGAUAACUAUACAACCUACUGCCUUCCCUGIn some applications, users may want to have a comprehensive investigation of a miRNA about the Name, Accession, Sequence, Precursor and mature miRNA information. The miRBaseConverter package embeds a useful function getMiRNAHistory() to retrieve all the detailed miRNA information in all miRBase historic version. Users can get a comprehensive overview of the miRNA.
#### 1. The input is a miRNA Name
name = "hsa-miR-26b-5p"
result1 = miRNA_NameToAccession(name)
Accession = result1$Accession
result2 = getMiRNAHistory(Accession)
result2
## Precursor PrecursorSequence Mature1 Mature1Sequence Mature2 Mature2Sequence Status
## v6 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> UNCHANGED
## v7_1 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> <NA>
## v8 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> UNCHANGED
## v8_1 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> UNCHANGED
## v8_2 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> UNCHANGED
## v9 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> UNCHANGED
## v9_1 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> UNCHANGED
## v9_2 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGUU <NA> <NA> UNCHANGED
## v10 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v10_1 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v11 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v12 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v13 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v14 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v15 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v16 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v17 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b* CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v18 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b-5p UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b-3p CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v19 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b-5p UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b-3p CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v20 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b-5p UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b-3p CCUGUUCUCCAUUACUUGGCUC UNCHANGED
## v21 hsa-mir-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGCUCGGGGACCGG hsa-miR-26b-5p UUCAAGUAAUUCAGGAUAGGU hsa-miR-26b-3p CCUGUUCUCCAUUACUUGGCUC UNCHANGED#### 2. The input is miRNA Accession Id
Accession = "MIMAT0000765"
result3 = getMiRNAHistory(Accession)
result3
## Precursor PrecursorSequence Mature1 Mature1Sequence Mature2 Mature2Sequence Status
## v6 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> UNCHANGED
## v7_1 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> <NA>
## v8 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> UNCHANGED
## v8_1 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> UNCHANGED
## v8_2 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> UNCHANGED
## v9 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> UNCHANGED
## v9_1 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> UNCHANGED
## v9_2 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU <NA> <NA> UNCHANGED
## v10 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v10_1 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v11 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v12 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v13 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v14 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v15 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v16 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v17 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335* UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v18 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335-5p UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335-3p UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v19 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335-5p UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335-3p UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v20 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335-5p UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335-3p UUUUUCAUUAUUGCUCCUGACC UNCHANGED
## v21 hsa-mir-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA hsa-miR-335-5p UCAAGAGCAAUAACGAAAAAUGU hsa-miR-335-3p UUUUUCAUUAUUGCUCCUGACC UNCHANGEDThere is a data table for presenting the detailed information of the defined miRNAs in each miRBase version. In miRBaseConverter package, we provide a function getMiRNATable() to return the miRNA data table for each miRBase version. Meanwhile, users can use the control parameter to custom the species in output.
library(miRBaseConverter)
miRNA_Tab=getMiRNATable(version="v21",species="hsa")
head(miRNA_Tab)
## Precursor_Acc Precursor Status Precursor_Seq Mature1_Acc Mature1 Mature1_Seq Mature2_Acc Mature2 Mature2_Seq
## 12741 MI0000060 hsa-let-7a-1 UNCHANGED UGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCACUGGGAGAUAACUAUACAAUCUACUGUCUUUCCUA MIMAT0000062 hsa-let-7a-5p UGAGGUAGUAGGUUGUAUAGUU MIMAT0004481 hsa-let-7a-3p CUAUACAAUCUACUGUCUUUC
## 12742 MI0000061 hsa-let-7a-2 UNCHANGED AGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUUACAUCAAGGGAGAUAACUGUACAGCCUCCUAGCUUUCCU MIMAT0000062 hsa-let-7a-5p UGAGGUAGUAGGUUGUAUAGUU MIMAT0010195 hsa-let-7a-2-3p CUGUACAGCCUCCUAGCUUUCC
## 12743 MI0000062 hsa-let-7a-3 UNCHANGED GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGGGAUAACUAUACAAUCUACUGUCUUUCCU MIMAT0000062 hsa-let-7a-5p UGAGGUAGUAGGUUGUAUAGUU MIMAT0004481 hsa-let-7a-3p CUAUACAAUCUACUGUCUUUC
## 12744 MI0000063 hsa-let-7b UNCHANGED CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCCCCUCGGAAGAUAACUAUACAACCUACUGCCUUCCCUG MIMAT0000063 hsa-let-7b-5p UGAGGUAGUAGGUUGUGUGGUU MIMAT0004482 hsa-let-7b-3p CUAUACAACCUACUGCCUUCCC
## 12745 MI0000064 hsa-let-7c UNCHANGED GCAUCCGGGUUGAGGUAGUAGGUUGUAUGGUUUAGAGUUACACCCUGGGAGUUAACUGUACAACCUUCUAGCUUUCCUUGGAGC MIMAT0000064 hsa-let-7c-5p UGAGGUAGUAGGUUGUAUGGUU MIMAT0026472 hsa-let-7c-3p CUGUACAACCUUCUAGCUUUCC
## 12746 MI0000065 hsa-let-7d UNCHANGED CCUAGGAAGAGGUAGUAGGUUGCAUAGUUUUAGGGCAGGGAUUUUGCCCACAAGGAGGUAACUAUACGACCUGCUGCCUUUCUUAGG MIMAT0000065 hsa-let-7d-5p AGAGGUAGUAGGUUGCAUAGUU MIMAT0004484 hsa-let-7d-3p CUAUACGACCUGCUGCCUUUCUIn miRBaseConverter package, the function goTo_miRBase() redirects users to the miRBase webpages of some specified miRNAs.
library(miRBaseConverter)
Accessions=miRNATest$Accession[1:10]
goTo_miRBase(Accessions)In miRBaseConverter package, the function goTo_miRNAFamily() redirects users to the miRBase miRNA family webpages of some specified miRNA families.
library(miRBaseConverter)
Accessions=miRNATest$Accession
Family_Info=checkMiRNAFamliy(Accessions)
FamilyAccessions=Family_Info$FamilyAccession[1:15]
goTo_miRNAFamily(FamilyAccessions)The R/Bioconductor package miRBaseConverter provides a suite of tools for checking miRNA Name, Accession, Sequence, Species, Version, Hisotry and Family information in different miRBase versions. We wish that the miRBaseConverter package could be a useful tool for miRNA research community and help to speed up the studies of miRNAs.
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