seqinr (version 3.3-3)

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

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

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