de novo assembly for mitochondrial genome

[mandar.bobade60]

Hi all,
I am working first time on de novo assembly. I am working on mitochondrial genome assembly of plant species. My expected genome size is about ~800KB and after velvet+AMOS use it is coming around ~1.1MB. I am further extending my analysis for gene prediction where I am currently stuck. I sought for your advices and help for gene prediction and annotation for Plant Mitochondrial genome. So far, I have used Mitofy but not sure of its result. Is RepeatModeler fine for plant mitochondrial genome?

Regards,
Mandar

[holmrenser]

Hi,

For annotating plant mitochondrial genomes mitofy seems fine, what is it that you doubt about the results? If you want to gain insight into the repeats present in your mitochondrial genome I guess RepeatModeler would be worth a try...

Cheers