Epilogue: Complications in ori Predictions

In this lesson, we’ve considered three genomes and found three different hypothesized 9-mers encoding DnaA boxes: ATGATCAAG in Vibrio cholerae, CCTACCACC in Thermotoga petrophila, and TTATCCACA in E. coli. We must warn you that finding ori is often more complex than we considered before. Some bacteria have even fewer DnaA boxes than E. coli, making it difficult to identify them. Some bacteria have even fewer DnaA boxes than E. coli, making it difficult to identify them.

Direction of ter region

The ter region is often located not directly opposite to ori but maybe significantly shifted, resulting in reverse and forward half-strands having substantially different lengths. The position of the skew minimum is often only a rough indicator of ori position, which forces researchers to expand their windows when searching for DnaA boxes, bringing in extraneous repeated substrings. Finally, skew diagrams don’t always look as nice as that of E. coli; for example, the skew diagram for Thermotoga petrophila is shown in the figure below: