Clustal Omega alignment algorithm - does it account for codons and open reading frames (ORF)?

Question

[manaswwm]

Hello all,

This might come across as a naive question: I performed a multiple sequence alignment of nucleotide sequences using the Clustal Omega tool of EBI (https://www.ebi.ac.uk/Tools/msa/clustalo/). As expected, the alignments have gaps in them. However do these multiple sequence alignment methods (in this case Clustal Omega) preserve open reading frames when introducing gaps? While looking at the output alignments I see that the gaps tend to be in multiples of 3 which gives me the idea that it is indeed preserving the open reading frames, but I wanted to confirm.

Thanks!

Answer 1

[Joe]

No, CLUSTAL has no knowledge of the ORFs in the input data. It just sees sequences. You might find that the codons appear to be somewhat preserved during the alignment, but thats just because they'll have conservation across the whole alignment to some degree.

It will not make any attempt to preserve reading frames.