Hi. This is my first time working with a full mitochondrial genome. This sequence was sequenced using Illumina and its consensus was produced using Geneious prime. My questions are:
1) After getting the consensus sequence, can I directly align and analyze the sequence or there are more steps that need to be done before that?
2) Do the steps to remove the stop codon is still the same when working with Sanger sequencing sequence? I know the steps when using MEGA and also read about Expasy. But, is there any other steps that is more suitable for a full mitogenome?
I see no need to remove the stop codons if you are comparing nucleotides unless you wish to stratify the analysis by codon position or you are for other reasons wishing to use only protein-coding genes. Depending on the organisms you are studying, the stop codons for the mitochondrial genes are known and you can can remove them if you wish. What organisms are your studying and for what purpose: phylogeny? selection analysis?Too little info here for an intelligent answer.
@patrice Sorry, I forgot to mention it. I am studying the rats and the purpose is to conduct a phylogenetic analysis by comparing several rats of different species, but the same genus. I would also do evolutionary analysis on the same sequences.
I am sure you know that the vertebrate mitochondrial codon table is different than nuclear DNA with TGA = Trp and not stop. But anyway, as Patrice has said, there is no reason to remove stop codons or any other bases, for phylogenetic analyses. Accurate alignment is key, and you may want to delete regions where you do not trust the alignment, but that should not be an issue in a narrow range of vertebrate genomes such as mammals. When you come to aligning fish, amphibians, lizards, snakes, birds and other vertebrates it can get difficult.
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