Introduction | Creating and accessing structure information | Creating a dot bracket annotation from base pairing information | Storing sequence and structure in one object | Session info | References
Package: Structstrings 1.29.0
Felix G.M. Ernst
Structstrings: Implementation of the dot bracket annotations with Biostrings
The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.
Authors:
Structstrings_1.29.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Structstrings/json (API)
| # Install 'Structstrings' in R: |
| install.packages('Structstrings', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/felixernst/structstrings/issues
On BioConductor:Structstrings-1.29.0(bioc 3.24)Structstrings-1.28.0(bioc 3.23)
dataimportdatarepresentationinfrastructuresequencingsoftwarealignmentsequencematchingbioconductorrnarna-structural-analysisrna-structuresequencesstructures
Last updated from:c0fda74d18. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 210 | ||
| linux-devel-arm64 | NOTE | 293 | ||
| linux-devel-x86_64 | NOTE | 354 | ||
| source / vignettes | OK | 286 | ||
| linux-release-arm64 | NOTE | 310 | ||
| linux-release-x86_64 | NOTE | 335 | ||
| macos-release-arm64 | NOTE | 196 | ||
| macos-release-x86_64 | NOTE | 284 | ||
| macos-oldrel-arm64 | NOTE | 177 | ||
| macos-oldrel-x86_64 | NOTE | 392 | ||
| windows-devel | NOTE | 214 | ||
| windows-release | NOTE | 244 | ||
| windows-oldrel | NOTE | 245 | ||
| wasm-release | OK | 428 |
Exports:alphabetcolnames<-convertAnnotationDBDBDFDBDFLDBSDBSLdotbracketDOTBRACKET_ALPHABETDOTBRACKET_CHAR_VALUESdotbracket<-DotBracketDataFrameDotBracketDataFrameListDotBracketStringDotBracketStringSetDotBracketStringSetListencodinggetBasePairinggetDotBracketgetLoopIndicesLoopIndexListreadDotBracketStringSetreadStructuredRNAStringSetsaveDotBracketStringSetSDBDFLseqtypeSplitDotBracketDataFrameListSTRUCTURE_CLOSE_CHRSTRUCTURE_NEUTRAL_CHRSTRUCTURE_OPEN_CHRStructuredRNAStringSetsubseqsubseq<-writeDotBracketStringSetwriteStructuredXStringSet
Dependencies:BiocGenericsBiostringsclicrayongenericsglueIRangeslifecyclemagrittrrlangS4VectorsSeqinfostringistringrvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert between dot bracket annotations | convertAnnotation convertAnnotation,DotBracketString-method convertAnnotation,DotBracketStringSet-method convertAnnotation,DotBracketStringSetList-method |
| DataFrame for storing base pairing information | CompressedSplitDotBracketDataFrameList-class CompressedSplitDotBracketDFrameList-class DBDF DBDFL DotBracketDataFrame DotBracketDataFrame-class DotBracketDataFrameList DotBracketDataFrameList-class DotBracketDFrame-class DotBracketDFrameList-class SDBDFL SimpleSplitDotBracketDataFrameList-class SimpleSplitDotBracketDFrameList-class SplitDotBracketDataFrameList |
| The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes | alphabet,DotBracketString-method DB DBS DBSL DotBracketString DotBracketString-class DotBracketStringSet DotBracketStringSet-class DotBracketStringSetList DotBracketStringSetList-class encoding,DotBracketString-method |
| Reading and writing DotBracketStringSet objects | DotBracketStringSet-io readDotBracketStringSet saveDotBracketStringSet writeDotBracketStringSet |
| Accessing Dot Bracket annotation | getBasePairing getBasePairing,DotBracketString-method getBasePairing,DotBracketStringSet-method getDotBracket getDotBracket,CompressedSplitDotBracketDataFrameList-method getDotBracket,DotBracketDataFrame-method getDotBracket,DotBracketDataFrameList-method getDotBracket,SimpleSplitDotBracketDataFrameList-method getLoopIndices getLoopIndices,CompressedSplitDotBracketDataFrameList-method getLoopIndices,DotBracketDataFrame-method getLoopIndices,DotBracketDataFrameList-method getLoopIndices,DotBracketString-method getLoopIndices,DotBracketStringSet-method getLoopIndices,SimpleSplitDotBracketDataFrameList-method |
| LoopIndexList: base pairing information as a list of integer values | LoopIndexList LoopIndexList-class |
| Structstrings: implementation of the dot bracket annotations with Biostrings | Structstrings |
| Structstrings example data | dbs nseq Structstrings-data |
| Structstrings internals | colnames<-,CompressedSplitDotBracketDataFrameList-method DOTBRACKET_ALPHABET DOTBRACKET_CHAR_VALUES seqtype,DotBracketString-method Structstrings-internals STRUCTURE_CLOSE_CHR STRUCTURE_NEUTRAL_CHR STRUCTURE_OPEN_CHR subseq,DotBracketString-method subseq<-,DotBracketString-method subseq<-,DotBracketStringSet-method [<-,DotBracketDataFrame-method |
| StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences | dotbracket dotbracket,StructuredXStringSet-method dotbracket<- dotbracket<-,StructuredXStringSet-method getBasePairing,StructuredXStringSet-method getLoopIndices,StructuredXStringSet-method readStructuredRNAStringSet StructuredRNAStringSet StructuredRNAStringSet-class StructuredXStringSet writeStructuredXStringSet |
