Oriloc

Prediction of origin and terminus of replication in bacteria

Description

Oriloc is described in the help page of the oriloc function of the seqinR package. Some graphical oriloc output examples are available there. More informations to help interpret the output is given there.

Download Oriloc

Source code of Oriloc and example files allowing to reproduce the figure in Frank and Lobry (2000) are available freely in the seqinR package. Download and install the seqinR package as any R package. More details in the documentation of the seqinR package which is available there on R-forge.

License

GPL version 2 or newer.

Big Room examples

Oriloc has been used to predict the origin of replication in the complete genomes of Bifidobacterium longum (Schell et al. 2002) and Blochmannia floridanus (Gil et al. 2003). Oriloc is also used in the Enhanced Microbial Genomes Library (EMBLib) to predict the origin and terminus of replication so as to add coding sequence orientation on the chromosome (i.e. whether the sense strand in on the leading or lagging strand for replication) under a new '/strand' qualifier in sequence data files (Perrière et al. 2000). This extra information was used in Lobry & Sueoka (2002) and in Daubin & Perrière (2003) to get insights on bacterial genome structures and evolution. For more graphical output examples see there.

References

If you use Oriloc in a published work, please cite the following reference:

Frank, C.A., Lobry, J.R. (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics, 16, 560-561.

A simple informal introduction to DNA-walks:

Lobry, J.R. (1999) Genomic landscapes. Microbiology Today, 26:164-165.

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.

History

Oriloc has been translated from C into the R implementation of the S langage for data manipulation and graphical display. Binaries are no more provided and the C source code is frozen. It is strongly recommended not tu use the outdated C version because the algorithm has been improved since then. This is exemplified in the figure given bellow. The black line represents the improvment in the new R version of Oriloc (the signal is smoothed thanks to a more approriate relative scaling of the GC-skew and of the AT-skew) as compared to the old C version.

Need help?

If you have any problems or comments about Oriloc, you can send an e-mail to the the seqinR-forum diffusion list. See instructions there.

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