How to identify mitochrondrial genes in DNA?

Question

[Ana]

Hi everyone,

Given a DNA sequence how to detect the mitochondrial genes? There's maybe some concepts of molecular biology that I'm not aware of, but I'm imagining that we have a full DNA sequence and in between it will result in different types of genes. I would like to know how I could find mitochondrial ones in particular from the whole sequence. I've found the two tables of universal and mitochrondial codes but I don't know how I could use them for this task.

Is it possible? How?

Thanks in advance,
Ana

[arnstrm]

What kind of DNA sequence do you have? FASTQ reads? scaffolds? genes? Easiest way would be to BLAST them against any database to see if they pick up mitochondrial genes (unless you have millions of fastq reads).

[Ana]

I currently have a directory with tophat output. As such I have a bam file and some bed ones with junctions, deletions and insertions.

Answer 1

[roy.granit]

Why not move on and run Cufflinks on the Tophat output to obtain the number of reads per gene? Then just you could simply sort for MT genes using the IDs you have, or extract the cellular compartment using BioMart..

• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
• BioMart