Assembly gene prediction/annotation of plant mitochondria
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9.7 years ago

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

Assembly genome gene • 4.1k views
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I think you should frame your question to include word "plant mitochondria", so that people can search your post using those key words.

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Good suggestion. Done !

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5.6 years ago
Shawrob400 ▴ 10

you can use these two tools.

NOVOPLASTY

NORGAL

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That's for assembly and not annotation.

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5.6 years ago
Tm ★ 1.1k

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.

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