oriloc {seqinr} | R Documentation

## Prediction of origin and terminus of replication in bacteria

### Description

This program finds the putative origin and terminus of replication in procaryotic genomes. The program works with unannotated sequences and therefore uses glimmer2 outputs to discriminate between codon positions.

### Usage

    oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
     g2.coord = system.file("sequences/ct.coord", package = "seqinr"),
    oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)

### Arguments

`seq.fasta` | the name of a file which contains the dna sequence of a bacterial chromosome in fasta format
`g2.coord` | the name of file which contains the output of glimmer2 program
`oldoriloc` | logical to be set at TRUE to reproduce the (deprecated) outputs of previous (publication date: 2000) version of the oriloc program
`gbk` | the URL of a file in GenBank format
`clean.tmp.files` | Logical, if TRUE temporary files are removed
`rot` | Integer, with zero default value, used to permute circurlarly the genome.

### Details

The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The program works with unannotated sequences in fasta format and therefore uses glimmer2.0 outputs to discriminate between codon positions so as to increase the signal/noise ratio.

### Value

A data.frame with seven columns: `g2num` for the CDS number in the `g2.coord` file, `start.kb` for the start position of CDS expressed in Kb (this is the position of the first occurence of a nucleotide in a CDS regardless of its orientation), `end.kb` for the last position of a CDS, `CDS.excess` for the DNA walk for gene orientation (+1 for a CDS in the direct strand, -1 for a CDS in the reverse strand) cummulated over genes, `skew` for the cummulated composite skew in third codon positions, `x` for the cummulated T - A skew in third codon position, `y` for the cummulated C - G skew in third codon positions.

### Note

The method works only for genomes having a single origin of replication from which the replication is bidirectional. To detect the composition changes, a DNA-walk is performed. In a 2-dimensional DNA walk, a C in the sequence corresponds to the movement in the positive y-direction and G to a movement in the negative y-direction. T and A are mapped by analogous steps along the x-axis. When there is a strand asymmetry, this will form a trajectory that turns at the origin and terminus of replication. Each step is the sum of nucleotides in a gene in third codon positions. Then ortogonal regression is used to find a line through this trajectory. Each point in the trajectory will have a corresponding point on the line, and the coordinates of each are calculated. Thereafter, the distances from each of these points to the origin (of the plane), are calculated. These distances will represent a form of cumulative skew. This permets us to make a plot with the gene position (gene number, start or end position) on the x-axis and the cumulative skew (distance) at the y-axis. Depending on where the sequence starts, such a plot will display one or two peaks. Positive peak means origin, and negative means terminus. In the case of only one peak, the sequence starts at the origin or terminus site.

### Author(s)

J.R. Lobry and A.C. Frank

### References

The original paper for oriloc:
Frank, A.C., Lobry, J.R. (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics, 16:566-567.
http://bioinformatics.oupjournals.org/cgi/reprint/16/6/560

A simple informal introduction to DNA-walks:
Lobry, J.R. (1999) Genomic landscapes. Microbiology Today, 26:164-165.
http://www.socgenmicrobiol.org.uk/QUA/049906.pdf

An early and somewhat historical application of DNA-walks:
Lobry, J.R. (1996) A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie, 78:323-326.

`citation("seqinr")`

### Examples

      ## Not run:   out <- oriloc()
      ## Not run:
      plot(out$st, out$sk, type="l", xlab="Map position in Kb",
        ylab = "Cumulated composite skew",
        main=expression(italic(Chlamydia~~trachomatis)~~complete~~genome))
    ## End(Not run)

[Package seqinr version 1.0-4 Index]