Circular chromosome of completed genome

[Apiwat Sangphukieo]

Dear all,

After I read the pseudo-code in the original paper "Prodigal: prokaryotic gene recognition and translation initiation site identification (2010)", I have a question about gene finding at the tail of circular chromosome. In the case of gene existing at the tail continuing to the head of chromosome, Prodigal can predict completed protein or not? For example, chromosome length is 1000 bp, a gene starts at position 990 and ends at position 10.  Can prodigal predict?

Thanks,

Apiwat Sangphukieo

[dhyatt1]

No, it does not have any flag for circular chromosomes.

Most people who assemble genomes just manually make sure base 1 of their finished chromosome isn't inside a gene.

You could use a tool like Circlator ( https://sanger-pathogens.github.io/circlator/ ), which circularizes assemblies and 

then actually uses prodigal to predict genes then moves base 1 to correspond to the start of a gene.

regards,

doug