FindOri: Detect the oriC region of a bacterial genome

In MarkoLebo/FindOri: Package for oriC detection and genomic signals display

Description

A function, that is used for oriC region detection in bacterial genomes

Usage

FindOri(sek)

Arguments

sek	a vector with nucleotide sequence of genome, saved in DNAString.

Value

returns a number of values in a list. In the first element of the list are parameters of the detected oriC region. The order of the parameteres are:

OriStart - position genome, where the oriC region starts,

OriEnd - position genome, where the oriC region starts,

OriLenght - length of the detected oriC,

OriGC - percentual GC-content of the oriC region,

OriAT - percentual AT-content of the oriC region,

Min - position of minimum of GC-disparity curve,

DnaAcount - number of detected DnaA-boxes in the detected oriC region.

The second element of the returning list is a vector called DistDnaA in which the distances of the beginning of each detected DnaA-box from the beginning of oriC is returned.

The last element of the returned list is the whole nucleotide sequence of the detected oriC region.

This function also displays the GC-disparity curve of the input genome.

Author(s)

Marko Lebo <[e-mail]>

Examples

## Not run: 
sek<-readDNAStringSet('sequence.fasta')
sek<-sek[[1]]
oriC <- FindOri(sek)

## End(Not run)

MarkoLebo/FindOri documentation built on May 7, 2019, 3:35 p.m.