LncFinder (version 1.1.6)

compute_FickettScore: Compute Fickett TESTCODE Score

Description

This function can compute Fickett TESTCODE score of DNA sequences proposed by James W.Fickett (Fickett JW. 1982). Fickett TESTCODE score can be calculated on full sequence or the longest ORF region.

Usage

compute_FickettScore(
  Sequences,
  label = NULL,
  on.ORF = FALSE,
  auto.full = FALSE,
  parallel.cores = 2
)

Value

A dataframe.

Arguments

Sequences

A FASTA file loaded by function read.fasta of seqinr-package.

label

Optional. String. Indicate the label of the sequences such as "NonCoding", "Coding".

on.ORF

Logical. If TRUE, Fickett TESTCODE score will be calculated on the longest ORF region.

auto.full

Logical. When on.ORF = TRUE but no ORF can be found, if auto.full = TRUE, Fickett TESTCODE score will be calculated on full sequences automatically; if auto.full is FALSE, the sequences that have no ORF will be discarded. Ignored when on.ORF = FALSE. (Default: FALSE)

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.

Author

HAN Siyu

Details

This function can compute Fickett TESTCODE score proposed by James W.Fickett (Fickett JW. 1982). Fickett TESTCODE score is selected as feature by method CPAT (Wang et al. 2013) and CPC2 (Kang et al. 2017). In CPAT, Fickett TESTCODE score is calculated on the longest ORF region, but CPC2 calculates the score on full sequence. This function compute_FickettScore improves the CPAT's code and is capable of computing the score on the longest ORF region as well as full sequence.

References

James W.Fickett. Recognition of protein coding regions in DNA sequences. Nucleic Acids Research, 1982, 10(17):5303-5318.

Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang & Ying Li. LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information, and physicochemical property. Briefings in Bioinformatics, 2019, 20(6):2009-2027.

Liguo Wang, Hyun Jung Park, Surendra Dasari, Shengqin Wang, JeanPierre Kocher & Wei Li. CPAT: coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Research, 2013, 41(6):e74-e74.

Yu-Jian Kang, De-Chang Yang, Lei Kong, Mei Hou, Yu-Qi Meng, Liping Wei & Ge Gao. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Research, 2017, 45(W1):W12-W16.

Examples

if (FALSE) {
data(demo_DNA.seq)
Seqs <- demo_DNA.seq

FickettScore <- compute_FickettScore(Seqs, label = NULL, on.ORF = TRUE,
                                     auto.full = TRUE, parallel.cores = 2)
}