run_RNAfold: Obtain the Secondary Structure Sequences Using RNAfold
In LncFinder: LncRNA Identification and Analysis Using Heterologous Features

Description Usage Arguments Details Value Author(s) See Also Examples

This function can compute secondary structure sequences. The tool "RNAfold" of software "ViennaRNA" is required for this function.

1	run_RNAfold(Sequences, RNAfold.path = "RNAfold", parallel.cores = 2)

`Sequences`	A FASTA file loaded by function `read.fasta` of `seqinr-package`.
`RNAfold.path`	String. Indicate the path of the program "RNAfold". By default is `"RNAfold"` for UNIX/Linux system. (See details.)
`parallel.cores`	Integer. The number of cores for parallel computation. By default the number of cores is `2`, users can set as `-1` to run this function with all cores.

This function is used to compute secondary structure. The output of this function can be used in function make_frequencies, extract_features, build_model and lnc_finder when parameter SS.features is set as TRUE.

This function depends on the program "RNAfold" of software "ViennaRNA". (http://www.tbi.univie.ac.at/RNA/index.html)

Parameter RNAfold.path can be simply defined as "RNAfold" as default when the OS is UNIX/Linux. However, for some OS, such as Windows, users need to specify the RNAfold.path if the path of "RNAfold" haven't been added in environment variables.

This function can print the related information when the OS is UNIX/Linux, such as:

"25 of 100, length: 695 nt",

which means around 100 sequences are assigned to this node and the program is computing the 25th sequence. The length of this sequence is 695nt.

If users have their own SS data, users can use function read_SS to load them, instead of obtaining from RNAfold.

Returns data.frame. The first row is RNA sequence; the second row is Dot-Bracket Notation of secondary structure sequences; the last row is minimum free energy (MFE).

HAN Siyu

read_SS

## Not run: 
### For a FASTA file contains several sequences,
### Use "read.fasta" function of package "seqinr" to read a FASTA file:
Seqs <- read.fasta(file =
"http://www.ncbi.nlm.nih.gov/WebSub/html/help/sample_files/nucleotide-sample.txt")

### Or just try to use our data "demo_DNA.seq"
data(demo_DNA.seq)
Seqs <- demo_DNA.seq

### Windows:
RNAfold.path <- '"E:/Program Files/ViennaRNA/RNAfold.exe"'
SS.seq_1 <- run_RNAfold(Seqs[1:2], RNAfold.path = RNAfold.path, parallel.cores = 2)

### For UNIX/Linux, "RNAfold.path" can be just defined as "RNAfold" as default:
SS.seq_2 <- run_RNAfold(Seqs, RNAfold.path = "RNAfold", parallel.cores = 2)

## End(Not run)