Mitochondrial genomes comparison

Question

[Gorysko]

Hi everybody

I have question - I need to compare two distinct mitochondrial proteoms (c.elegans and melanogaster )

I was trying to find some suitable approach or way of comparing - but failed

Maybe here someone could give advice about approach ?

Answer 1

[Adrian Pelin]

extract CDS regions and do a codon alignment. Also, figure out absence/presence of genes. This all depends on why are you comparing the two mitochondrial genomes in the first place. And by the way, there is a big difference between mitochondrial genome and mitochondrial proteome.

[Gorysko]

@Andrian Pelin - YesI know that it's big difference , I was usring BRH ( best reciprocal hit ), and as result I've got quite strange results

[Adrian Pelin]

it will be helpful if you start showing what you did and what you got.

[Gorysko]

I've took two genomes ( c.elegans and melanogaster ), and proceeded them with BRH ( best reciprocal hit ) - blasting each gene in first genome against each gene in second and vice versa , if best result the same it's a match.

After such manipulations I've got only 9 genes

[Adrian Pelin]

Yes but mitochondrial genomes are very compact (especially in animals), the amount of genes in those genomes are very limited, cox, atp and nadh family genes and cob. That's pretty much it. You don't need to use blast from one to find the genes in the other, I am sure both mtDNA of c.elegans and drosophilas are published and well annotated.