This program finds the putative origin and terminus of replication in procaryotic genomes. The program discriminates between codon positions.
oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"),
g2.coord = system.file("sequences/ct.predict", package = "seqinr"),
glimmer.version = 3,
oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)Character: the name of a file which contains the DNA sequence
of a bacterial chromosome in fasta format. The default value,
system.file("sequences/ct.fasta.gz", package ="seqinr") is
the fasta file ct.fasta.gz. This is the file
for the complete genome sequence of Chlamydia trachomatis
that was used in Frank and Lobry (2000). You can replace
this by something like seq.fasta = "myseq.fasta" to work
with your own data if the file myseq.fasta is present in
the current working directory (see getwd), or give
a full path access to the sequence file (see file.choose).
Character: the name of file which contains the output of
glimmer program (*.predict in glimmer version 3)
Numeric: glimmer version used, could be 2 or 3
Logical: to be set at TRUE to reproduce the (deprecated) outputs of previous (publication date: 2000) version of the oriloc program.
Character: the URL of a file in GenBank format. When provided
oriloc use as input a single GenBank file instead of the seq.fasta
and the g2.coord. A local temporary copy of the GenBank file is
made with download.file if gbk starts with
http:// or ftp:// or file:// and whith
file.copy otherwise. The local copy is then used as
input for gb2fasta and gbk2g2 to produce
a fasta file and a glimmer-like (version 2) file, respectively, to be used
by oriloc instead of seq.fasta and g2.coord .
Logical: if TRUE temporary files generated when working with a GenBank file are removed.
Integer, with zero default value, used to permute circurlarly the genome.
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.
The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The programs works only with third codon positions so as to increase the signal/noise ratio. To discriminate between codon positions, the program use as input either an annotated genbank file, either a fasta file and a glimmer2.0 (or glimmer3.0) output file.
More illustrated explanations to help understand oriloc outputs are available there: https://pbil.univ-lyon1.fr/software/Oriloc/howto.html.
Examples of oriloc outputs on real sequence data are there: https://pbil.univ-lyon1.fr/software/Oriloc/index.html.
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. https://doi.org/10.1093/bioinformatics/16.6.560
A simple informal introduction to DNA-walks: Lobry, J.R. (1999) Genomic landscapes. Microbiology Today, 26:164-165. https://seqinr.r-forge.r-project.org/MicrTod_1999_26_164.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.
Glimmer, a very efficient open source software for the prediction of CDS from scratch in prokaryotic genome, is decribed at http://ccb.jhu.edu/software/glimmer/index.shtml. For a description of Glimmer 1.0 and 2.0 see:
Delcher, A.L., Harmon, D., Kasif, S., White, O., Salzberg, S.L. (1999) Improved microbial gene identification with GLIMMER, Nucleic Acids Research, 27:4636-4641.
Salzberg, S., Delcher, A., Kasif, S., White, O. (1998) Microbial gene identification using interpolated Markov models, Nucleic Acids Research, 26:544-548.
citation("seqinr")
# NOT RUN {
#
# A little bit too long for routine checks because oriloc() is already
# called in draw.oriloc.Rd documentation file. Try example(draw.oriloc)
# instead, or copy/paste the following code:
#
out <- oriloc()
plot(out$st, out$sk, type = "l", xlab = "Map position in Kb",
ylab = "Cumulated composite skew",
main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome))
#
# Example with a single GenBank file:
#
out2 <- oriloc(gbk="ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.gbk")
draw.oriloc(out2)
#
# (some warnings are generated because of join in features and a gene that
# wrap around the genome)
#
# }
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