[Seqinr-forum] Prediction of replication terminus

[Jean Lobry]

Hi Xiaojun,

predictions based on skews can only predict chirochore
boundaries but no which is the origin and the terminus. There
is a general but not universal trend in GC skew that
may help but in your case there is almost no contribution
of the GC skew to the combined skew.

Based on the strong signal at 400 kb and the CDS orientation
bias my guess would be that the origin is there.

Best,

Jean Lobry

Le 02/12/2020 à 02:28, Xiaojun Wang a écrit :
> Hi all,
> 
> My purpose is to predict the replication terminus for archaea, 
> Thermococcus eurythermalis A501 (NZ_CP008887). So I used Oriloc to do 
> the cumulative GC skew, which showed that the terminus is around at 
> 400kb (lowest value corresponds to the terminus of replication according 
> to their manual, see attached fig 1).
> 
> However, when I used Ori-Finder2, another software to predict the origin 
> of replication, it told me the replication origin is  from 425,719 to 
> 426,421 (see attached fig 2), which is very close to the terminus by Oriloc.
> 
> It looks like the origin overlaps with the terminus, I don’t think it is 
> reasonable.
> 
> Would you please let me know if my interpretation is correct? Do you 
> have any suggestions on the prediction of the terminus? Thanks a lot!
> 
> Best regards,
> 
> Xiaojun
> 
> 
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