seqinr (version 3.1-2)

recstat: Prediction of Coding DNA Sequences.

Description

This function aims at predicting the position of Coding DNA Sequences (CDS) through the use of a Correspondence Analysis (CA) computed on codon composition, this for the three reading frames of a DNA strand.

Usage

recstat(seq, sizewin = 90, shift = 30, seqname = "no name")

Arguments

seq

a nucleic acid sequence as a vector of characters

sizewin

an integer, multiple of 3, giving the length of the sliding window

shift

an integer, multiple of 3, giving the length of the steps between two windows

seqname

the name of the sequence

Value

• This function returns a list containing the following components:
• seq
  a single DNA sequence as a vector of characters
• sizewin
  length of the sliding window
• shift
  length of the steps between windows
• seqsize
  length of the sequence
• seqname
  name of the sequence
• vdep
  a vector containing the positions of windows starts
• vind
  a vector containing the reading frame of each window
• vstopd
  a vector of stop codons positions in direct strand
• vstopr
  a vector of stop codons positions in reverse strand
• vinitd
  a vector of start codons positions in direct strand
• vinitr
  a vector of start codons positions in reverse strand
• resd
  a matrix containing codons frequencies for all the windows in the three frames of the direct strand
• resr
  a matrix containing codons frequencies for all the windows in the three frames of the reverse strand
• resd.coa
  list of class coa and dudi containing the result of the CA computed on the codons frequencies in the direct strand
• resr.coa
  list of class coa and dudi containing the result of the CA computed on the codons frequencies in the reverse strand

Details

The method is built on the hypothesis that the codon composition of a CDS is biased while it is not the case outside these regions. In order to detect such bias, a CA on codon frequencies is computed on the six possible reading frames of a DNA sequence (three from the direct strand and three from the reverse strand). When there is a CDS in one of the reading frame, it is expected that the CA factor scores observed in this frame (fot both rows and columns) will be significantly different from those in the two others.

References

The original paper describing recstat is: Fichant, G., Gautier, C. (1987) Statistical method for predicting protein coding regions in nucleic acid sequences. Comput. Appl. Biosci., 3, 287--295. http://bioinformatics.oxfordjournals.org/content/3/4/287.abstract

See Also

draw.recstat, test.li.recstat, test.co.recstat

Examples

library(seqinr)
library(ade4)
ff <- system.file("sequences/ECOUNC.fsa", package = "seqinr2")
seq <- read.fasta(ff)
rec <- recstat(seq[[1]], seqname = getName(seq))