A Sort-based Algorithm for Multiple Sequence Alignment *
نویسنده
چکیده
We propose a sort-based algorithm for multiple sequence alignment using anchors. Anchors are determined by the use of suffix sorting along with position-based sorts. Potential anchor points are identified by a careful exploitation of the sorted suffixes obtained from a generalized suffix array of the input sequences. Final alignment is obtained by a recursive application of the suffix-sorting and position-based sort procedures. The basis of our approach is the recent result in linear-time worst-case suffix sorting and the implicit gap induction during the anchor point computation process. Implicit gap induction eliminates the need for the usual exhaustive search required for gap insertion during alignment. Suffix sorting and implicit gap induction have direct consequences on the overall complexity of the proposed alignment algorithm. We believe that the proposed approach could provide some new insights in the problem of multiple sequence alignment.
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