Hi everyone,
A naive question probably as I am not an expert in multiple alignement.
I would like to know if it is possible to align multiple proteins, allowing gaps in all of the sequence to be align except one ? I was thinking maybe I can put a very high gap penalty but gap penalties are always applied on all the sequence when starting the alignement, not only one.
I am familiar with MEGA or Jalview and the various algorithm disponibles (ClustalW/O, MUSCLE, MAFFT…) but I could not see any option to prevent gap in one sequence only.
Ok thank you, I was trying to figure out if it was possible to keep one sequence gap-free but while doing so I understood it is not possible. Thanks!
However,
I guess I was confuse with the following:
Between those two sequences, the best align is the following (obviously)
A—STGLVPY (1)
AGSTGLVPY (2)
However, if we don't know (evolutionary speaking) whether the first sequence was the ancestral one and the second sequence the mutated one, (or inversely), how could we assume that G was deleted in (1) or inserted in (2) ? We cannot, right?
So a gap — is not representative of a deletion, nor an insertion. It could be one or the other. I guess that is why we say indels ?
I think my confusion was coming from the gap symbol — which made me think that it was a representation of a deletion.
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