We have an msa based on k sequences. We want to generate a new msa based on k + 1 sequences . What is the most efficient way to get there? What would be inefficient?

Question

[wpkt92]

My guess is this:

Efficient: ClustalW

Inefficient: dynamic programming

Is this correct? i also need some explanation. Thanks!

Answer 1

[Jean-Karim Heriche]

Dynamic programming is an algorithmic technique used by almost all sequence aligners, including ClustalW.
Multiple sequence alignment based only on dynamic programming is not practical so MSA programs use heuristics to reduce the computational complexity at the cost of some loss of accuracy.
Now if you already have an MSA with k sequences, the most economical way to do k+1 sequences is simply to add the one sequence to the existing MSA.
By the way, if efficiency is an issue, have a look at Clustal Omega.