Aligning Mitochondrial Dna

Question

[Ehamberg]

When downloading mammal mitochondrial genomes (circular DNA) from NCBI, do they have a conventional sequence start point such that it makes sense to align a set of mtDNA genomes?

If so: Does this extend to other classes such as ray-finned fishes as well? (I.e.; could such mitochondrial genomes be included in an alignment as well?)

The aligned sequences are to be used to test a phylogeny inference system.

I would be happy to be pointed to more information on this.

[David W]

Don't know about a ref. alignment but this q. might help if you have to align mt genomes with different starting points.

Answer 1

[Larry_Parnell]

There is indeed a conventional start site or position 1 for human mitochondrial DNA. Please note that there is likely to be many more human sequences for the MT genome in data repositories - public and private - than all other mammalian MT genomes combined. This is due to the maternal heritability of this genome. As far as extension to ray-finned fishes for teh conventional placement of position 1, I am not certain. This would be easy to determine by simple one-to-one alignment of the fish DNA sequence to the human, or by good annotation of the fish MT genome - where you look to compare the order of the encoded genes.