Does Nucleotide Alignment can Translate into Proteins (Amino Acids)?

Question

[pfee418]

Hi guys, I did multiple sequence alignment (MSA) on all human coronaviruses (8579 nucleotide sequences). I would like to translate the nucleotide alignment into proteins, is it possible? I am still new to this field so I do not have any advanced knowledge on this :'D

I thought it is possible at first but I am thinking if that particular codon (3 nucleotides) is separated by gaps in between them. For example, atg is a codon and it looks like this (a--tg) which there are gaps in between the codon. Does translation into proteins is possible in this case?

Can anyone provide any opinions and views on this? Thank you in advanced for all the suggestions and explanations and I do appreciate all the responses I'll be receiving. :)))

[Mensur Dlakic]

What do you think about translating nucleotide sequences into proteins, and aligning those instead? Even if what you want to do is possible, most likely you will not get a good alignment unless the sequences are highly similar.

[Dunois]

Hmm just out of curiosity, what would be the (biological) implications of a gap in the alignment of a bunch of start codons? Frameshifts?

Answer 1

[ehsansepahi]

This is my suggestion:

Tools like EMBOSS getorf or sixpack find all ORFs (Open Reading Frames) based on your options in a sequence (in your case 8579 sequences). You can opt to output ORFs in nucleic acid or amino acid sequences. Then, cluster your ORF sequences based on similarity (using pairwise alignments between ORFs of different sequences (not ORFs of a sequences), etc...) and then do MSA on each cluster.