Assembly gene prediction/annotation of plant mitochondria

Question

[mandar.bobade]

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

[Tm]

I think you should frame your question to include word "plant mitochondria", so that people can search your post using those key words.

[lakhujanivijay]

Good suggestion. Done !

Answer 1

[Shawrob400]

you can use these two tools.

NOVOPLASTY

NORGAL

[Tm]

That's for assembly and not annotation.

Answer 2

[Tm]

You can use Geseq which is web based tool and easy to use. It works well with both mitochondria and chloroplast.

You can also go through the list of other alternative tools for annotation, provided on geseq website itself.