Question: How to identify mitochrondrial genes in DNA?
0
gravatar for Ana
5.1 years ago by
Ana20
Portugal
Ana20 wrote:

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

mitochondrial gene • 1.1k views
ADD COMMENTlink modified 5.1 years ago by roy.granit830 • written 5.1 years ago by Ana20

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).

 

ADD REPLYlink written 5.1 years ago by arnstrm1.8k

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

ADD REPLYlink written 5.1 years ago by Ana20
1
gravatar for roy.granit
5.1 years ago by
roy.granit830
Israel/LabWorm
roy.granit830 wrote:

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

 

 

 

ADD COMMENTlink written 5.1 years ago by roy.granit830
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