#BioinformaticsTool: OriFinder

15 Jul 2017

OriFinder is a web-based tool that predicts the location of the origin of replication in bacterial genomes (OriC).

 

It consists of several programs, each with output indicating different factors that enable prediction of OriC:

  • Plotting RY-, MK-, GC- and AT-skew [1] (see here for details)

  • Finding DnaA boxes*

  • Calculating priority ranks for every intergenic sequence

  • Predicting genes using ZCURVE 1.02 [2] if a PTT file is not provided by the user (via GenBank or otherwise); these can then be BLAST'd against a database of OriC-related gene sequences such as dnaA, dnaN, hemE, gidA + more. [3]

*When locating DnaA boxes, the program defaults to searching the most well studied, which occur in E. coli + have the sequence TTATCCACA. The user can also select for species-specific DnaA boxes from a list of sequences previously reported for the species or for those closely related to them. Alternatively, custom sequences can be defined. Most importantly, note that OriFinder also searches for sequences of length nine that differ from the input sequence by one base; this can be altered according to the user's needs.

 

The authors comment that methods using on GC-skew analysis + dnaA gene/box location information can only predict OriC in 60% of bacterial genome in GenBank. Their integrated method, on the other hand, claims to provide reliable OriC locus predictions for 98% of them.

 

[195]

 

This post is based on the following paper:

Gao, F. and Zhang, C.T., 2008. Ori-Finder: a web-based system for finding oriC s in unannotated bacterial genomes. BMC bioinformatics, 9(1), p.79.

 

References

1. Zhang, R. and Zhang, C.T., 2005. Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea, 1(5), pp.335-346.

2. Guo, F.B., Ou, H.Y. and Zhang, C.T., 2003. ZCURVE: a new system for recognizing protein‐coding genes in bacterial and archaeal genomes. Nucleic acids research, 31(6), pp.1780-1789.

3. Ogasawara, N. and Yoshikawa, H., 1992. Genes and their organization in the replication origin region of the bacterial chromosome. Molecular microbiology, 6(5), pp.629-634.

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