predictStructure: Return list of predicted secondary structure

In JackXu2333/dseAnalysis: Correlation analysis of RNA secondary structure mutation and differential expression

Description

Perform RNA structural prediction based on fasta file or input of RNA name and sequence. Secondary structure prediction algorithm based on command line program RNAStructure from Mathews Lab, program require current path to the executable, MacOS or Unix based user installed entire package is allowed to omit.

Usage

predictStructure(
  executable.path = "",
  fasta.file = "",
  rna.name = c(),
  rna.seq = c()
)

Arguments

executable.path	The path referred to RNAStructure executable (.../RNAStructure/exe) used by program
fasta.file	The file path with mature sequences in fasta format
rna.name	List consisted with name of the RNA sequence in seq
rna.seq	List consisted with RNA sequence

Value

Returns a list of dot bracket form, ordered according to the input name sequence

Author(s)

Sijie Xu, [e-mail]

References

Duan, S., Mathews, D.H. and Turner, D.H. (2006). Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA. Biochemistry, 45:9819-9832.

Wuchty, S., Fontana, W., Hofacker, I.L. and Schuster, P. (1999). Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49:145-165.

Examples

## Not run: dot <- predictStructure(executable.path = "./exe"
                                 , rna.name = c("hsa-let-7b", "hsa-let-7a-2")
                                 , rna.seq = c("UGGGAUGAGGUGGAUGUCUUUCCUA", "GAUAACUAUACAAUCUAC"))
## End(Not run)

JackXu2333/dseAnalysis documentation built on Dec. 31, 2020, 1:09 p.m.