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Old 10-22-2014, 01:46 AM   #1
Location: India

Join Date: Jun 2013
Posts: 14
Default de novo assembly for mitochondrial genome

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?

mandar.bobade60 is offline   Reply With Quote
Old 10-23-2014, 01:54 AM   #2
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Location: Netherlands

Join Date: Jul 2013
Posts: 9


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...

holmrenser is offline   Reply With Quote

annotation, assembly

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