readCT: Reads a file with the secondary structure of an RNA in the CT...

In ncRNAtools: An R toolkit for non-coding RNA

Description

Reads a file with the secondary structure of an RNA in the CT format (Connectivity Table).

Usage

readCT(filename, sequence=NULL)

Arguments

filename

A string indicating the path to the CT file to be read. A description of the CT format can be found at http://rna.urmc.rochester.edu/Text/File_Formats.html#CT. The CT file should contain information for all nucleotides of the RNA sequence, including those that do not form base pairs, unless the full-length RNA sequence is provided through the sequence argument. In such case, the CT file may contain only information for nucleotides involved in base pairs.

sequence

A string with the full-length sequence of the RNA whose secondary structure is represented in the CT file. Such argument is optional, but if it is not provided, a complete CT file with information for all nucleotides of the RNA must be provided.

Value

A list with the following 4 elements:

sequenceName	name of the RNA sequence
sequence	RNA sequence
sequenceLength	number of nucleotides of the RNA sequence
pairsTable	a dataframe indicating the paired bases, in the same format as that returned by the findPairedBases function

References

http://rna.urmc.rochester.edu/Text/File_Formats.html#CT.

Examples

exampleCTFile <- system.file("extdata", "exampleCT.ct", package="ncRNAtools")

# If the CT file does not contain information for unpaired nucleotides, the
# original sequence must also be supplied in order to read it (tmRNA of E. coli 
# encoded by the ssrA gene):

tmRNASequence <- "GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGG
CCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCU
CUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUU
GAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUAA
GCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA"

tmRNASecondaryStructure <- readCT(exampleCTFile, tmRNASequence)

Example output

ncRNAtools documentation built on Nov. 8, 2020, 8:14 p.m.