A putative origin of both 1Dx2s and 1Dx2f genes indicated that they could be originated from one octapeptide deletion and two unequal cross-over events.
The putative origin of replication possesses all characteristic features of the theta mechanism for replicating plasmids.
Analyzing the recent high-quality genome sequence of the domestic dog (Canis lupus familiaris), we deduced for the first time in a mammalian species belonging to Carnivora order, the genomic structure and the putative origin of the TRG locus.
The putative origin of replication consisted of a cluster of CDS comprising dnaA, dnaN, recF and gyrAB.
Therefore, the putative origin was determined from analysis of the GC skew (G−C/G+C) [63].
All sequences were then reordered to a putative origin adjacent to the replication initiation gene (repA) as described for the homolog replicon of B. anthracis plasmid pXO2 [29] and automatically annotated using the GenDB system [58].
Then, the putative origin of each ancestral sequence (i.e. internal node) in the tree was inferred with the Fitch algorithm by finding the most parsimonious reconstruction (MPR) of the ancestral character.
We predicted the putative origin of replication (oriV) of pRF (Figure 4) based on results from GenSkew (http://mips.gsf.de/services/analysis/genskew), an application for computing and plotting nucleotide skew data.
Regions representing the putative origin of replication (ori) and termination (ter) were predicted by Ori-Finder software [216] that combines gene finding, detection of base composition assymetry (e.g. GC-skew), and analysis of DnaA-box distribution.
Then, the putative origin of each ancestral sequence (i.e. internal node) in the tree is inferred by finding the most parsimonious reconstruction (MPR) of the ancestral character (supplemental Figure S3).
We identified the putative origin of replication (oriV) of pRF (Figure 4) based on results from GenSkew (http://mips.gsf.de/services/analysis/genskew), an application for computing and plotting nucleotide skew data.
