Question: Assembly gene prediction/annotation of plant mitochondria
0
gravatar for mandar.bobade
4.2 years ago by
India
mandar.bobade20 wrote:

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

gene assembly genome • 1.6k views
ADD COMMENTlink modified 5 weeks ago by Vijay Lakhujani3.5k • written 4.2 years ago by mandar.bobade20

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

ADD REPLYlink written 5 weeks ago by toralmanvar730

Good suggestion. Done !

ADD REPLYlink written 5 weeks ago by Vijay Lakhujani3.5k
1
gravatar for Shawrob400
5 weeks ago by
Shawrob40010
Chittagong Veterinary and Animal Sciences University
Shawrob40010 wrote:

you can use these two tools.

NOVOPLASTY

NORGAL

ADD COMMENTlink written 5 weeks ago by Shawrob40010

That's for assembly and not annotation.

ADD REPLYlink written 5 weeks ago by toralmanvar730
1
gravatar for toralmanvar
5 weeks ago by
toralmanvar730
toralmanvar730 wrote:

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.

ADD COMMENTlink written 5 weeks ago by toralmanvar730
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