sequence alignment by genetic algorithm

sequence alignment by genetic algorithm

We describe a new approach to multiple sequence alignment using genetic algorithms and an associated software package called SAGA. The method involves evolving a population of alignments in a quasi evolutionary manner and gradually improving the fitness of the population as measured by an objective function which measures multiple alignment quality. SAGA uses an automatic scheduling scheme to control the usage of 22 different operators for combining alignments or mutating them between generations. When used to optimise the well known sums of pairs objective function, SAGA performs better than some of the widely used alternative packages. This is seen with respect to the ability to achieve an optimal solution and with regard to the accuracy of alignment by comparison with reference alignments based on sequences of known tertiary structure. The general attraction of the approach is the ability to optimise any objective function that one can invent.


The simultaneous alignment of many nucleic acid or amino acid sequences is one of the most commonly used techniques in sequence analysis. Multiple alignments are used to help predict the secondary or tertiary structure of new sequences; to help demonstrate homology between new sequences and existing families; to help find diagnostic patterns for families; to suggest primers for PCR and as an essential prelude to phylogenetic reconstruction. The great majority of automatic multiple alignments are now carried out using the `progressive’ of Feng and Doolittle ( 1 ) or variations on it ( 2 – 4 ). This approach has the great advantage of speed and simplicity combined with reasonable sensitivity as judged by the ability to align sets of sequences of known tertiary structure. The main disadvantage of this approach is the `local minimum’ problem which stems from the greedy nature of the algorithm. This means that if any mistakes are made in any intermediate alignments, these cannot be corrected later as more sequences are added to the alignment. Further, there is no objective function (a measure of overall alignment quality) which can be used to say that one alignment is preferable to another or to say that the best possible alignment, given a set of parameters, has been found.

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