readDotBracket: Reads a file with the sequence and secondary structure of an...

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

readDotBracket(filename)

Arguments

filename

A string indicating the path to the Dot-Bracket file to be read. A description of the Dot-Bracket format can be found at https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html. Both basic and extended Dot-Bracket notations are accepted. The Dot-Bracket file should always contain at least two lines: the first one with the RNA sequence, and the second one with the secondary structure representation. The free energy of the secondary structure can be optionally present at the end of the secondary structure line, in kcal/mol. An additional optional line can precede these two, containing ">" as its first character followed by the name or description of the sequence.

Value

A list with the following 4 elements:

sequenceName	name of the RNA sequence. Will be set to NA if no string starting with ">" is present at the beginning of the Dot-Bracket file
sequence	RNA sequence
secondaryStructure	string representing the secondary structure of the RNA in the Dot-Bracket format
freeEnergy	free energy of the secondary structure of the RNA, usually in kcal/mol. If not present in the Dot-Bracket file, it will be set to NA

References

https://software.broadinstitute.org/software/igv/RNAsecStructure

http://projects.binf.ku.dk/pgardner/bralibase/RNAformats.html

Examples

exampleDotBracketFile <- system.file("extdata", "exampleDotBracket.dot", 
                                     package="ncRNAtools")

exampleDotBracket <- readDotBracket(exampleDotBracketFile)

# Since the file does not contain an initial line with the name of the sequence,
# sequenceName is set to NA

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