## ----setup, echo=FALSE-------------------------------------------------------- knitr::opts_chunk$set(message=FALSE, fig.path='figures/') ## ----include = FALSE---------------------------------------------------------- library(rfaRm) library(rsvg) library(R4RNA) library(treeio) ## ----tidy = TRUE-------------------------------------------------------------- rfamTextSearchFamilyAccession("riboswitch") ## ----tidy = TRUE, tidy.opts=list(width.cutoff = 80)--------------------------- sequenceSearch <- rfamSequenceSearch("GGAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGUGGUAUAGUCCACGAAAGUAUUUGCUUUGAUUUGGUGAAAUUCCAAAACCGACAGUAGAGUCUGGAUGAGAGAAGAUUC") length(sequenceSearch) names(sequenceSearch) ## Save the aligned consensus sequence and query sequence to a text file, together with secondary structure annotation writeLines(c(sequenceSearch$FMN$alignmentQuerySequence, sequenceSearch$FMN$alignmentMatch, sequenceSearch$FMN$alignmentHitSequence, sequenceSearch$FMN$alignmentSecondaryStructure), con="searchAlignment.txt") ## ----tidy = TRUE-------------------------------------------------------------- rfamFamilyAccessionToID("RF00174") rfamFamilyIDToAccession("FMN") ## ----tidy = TRUE-------------------------------------------------------------- rfamFamilySummary("RF00174") # The summary includes, amongst other data, a brief paragraph describing the family rfamFamilySummary("RF00174")$comment ## ----tidy = TRUE-------------------------------------------------------------- rfamConsensusSecondaryStructure("RF00174", format="WUSS") rfamConsensusSecondaryStructure("RF00174", format="DB") rfamConsensusSecondaryStructure("RF00174", filename="RF00174secondaryStructure.txt", format="DB") ## ----tidy = TRUE, echo = TRUE, results = 'hide'------------------------------- secondaryStructureTable <- readVienna("RF00174secondaryStructure.txt") plotHelix(secondaryStructureTable) ## ----tidy = TRUE, echo = TRUE, results = 'hide'------------------------------- ## Retrieve an SVG with a normal representation of the secondary structure of Rfam family RF00174 and store it into a character string, which can be read by rsvg after conversion from SVG string to raw data normalSecondaryStructureSVG = rfamSecondaryStructureXMLSVG("RF00174", plotType="norm") rsvg(charToRaw(normalSecondaryStructureSVG)) ## Retrieve an SVG with a sequence conservation representation added to the secondary structure of Rfam family RF00174, and save it to an SVG file rfamSecondaryStructureXMLSVG("RF00174", filename="RF00174SSsequenceConservation.svg", plotType="cons") ## ----tidy = TRUE, echo = TRUE, results = 'hide'------------------------------- ## Plot a normal representation of the secondary structure of Rfam family RF00174 rfamSecondaryStructurePlot("RF00174", plotType="norm") ## ----tidy = TRUE, echo = TRUE, results = 'hide'------------------------------- ## Save to a PNG file a plot of a representation of the secondary structure of Rfam family with ID FMN with sequence conservation annotation rfamSecondaryStructurePlot("RF00050", filename="RF00050SSsequenceConservation.png", plotType="cons") ## ----tidy = TRUE-------------------------------------------------------------- rfamSeedAlignment("RF00174", filename="RF00174seedAlignment.stk", format="stockholm") rfamSeedAlignment("RF00174", filename="RF00174seedAlignment.stk", format="fasta") ## ----tidy = TRUE, echo = TRUE, results = 'hide'------------------------------- seedTreeNHXString <- rfamSeedTree("RF00050", filename="RF00050tree.nhx") treeioTree <- read.nhx("RF00050tree.nhx") ## ----tidy = TRUE, echo = TRUE, results = 'hide'------------------------------- rfamSeedTreeImage("RF00164", filename="RF00164seedTreePlot.png", label="species") ## ----tidy = TRUE, echo = TRUE, results = 'hide'------------------------------- rfamCovarianceModel("RF00050", filename="RF00050covarianceModel.cm") ## ----tidy = TRUE-------------------------------------------------------------- ## By providing a filename, the sequence regions will be written to a tab-delimited file sequenceRegions <- rfamSequenceRegions("RF00050", "RF00050sequenceRegions.txt") head(sequenceRegions) ## ----tidy = TRUE-------------------------------------------------------------- ## By providing a filename, the matching PDB entries will be written to a tab-delimited file PDBentries <- rfamPDBMapping("RF00050", "RF00050PDBentries.txt") PDBentries