How do you determine protein-coding genes in mitochondrial genome?

12 December 2013 1 7K Report

I have the finished mitochondrial genome by de novo assembly with next-generation sequencing data. While annotating protein-coding gene in the mitochondrial genome, I use MITOS and DOGMA to predict the regions of protein-coding genes. In addition, I also use blastn and tblastn with reference genome for validation. Unfortunately, there is no consistent result among MITOS, DOGMA, blastn and tblastn. Any input is welcome.

Antony T Vincent

You can use homemade script using BioPerl or BioPython module.

You can also use augustus and artemis. You may take a look at some genome browser, there is list:

http://en.wikipedia.org/wiki/Genome_browser

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