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  The practical use of the A* algorithm for exact multiple sequence alignment

Lermen, M., & Reinert, K.(1997). The practical use of the A* algorithm for exact multiple sequence alignment (MPI-I-97-1-028).

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 Creators:
Lermen, Martin1, Author           
Reinert, Knut1, Author           
Affiliations:
1Algorithms and Complexity, MPI for Informatics, Max Planck Society, ou_24019              

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 Abstract: Multiple alignment is an important problem in computational biology. It is well known that it can be solved exactly by a dynamic programming algorithm which in turn can be interpreted as a shortest path computation in a directed acyclic graph. The $\cal{A}^*$ algorithm (or goal directed unidirectional search) is a technique that speeds up the computation of a shortest path by transforming the edge lengths without losing the optimality of the shortest path. We implemented the $\cal{A}^*$ algorithm in a computer program similar to MSA~\cite{GupKecSch95} and FMA~\cite{ShiIma97}. We incorporated in this program new bounding strategies for both, lower and upper bounds and show that the $\cal{A}^*$ algorithm, together with our improvements, can speed up comput ations considerably. Additionally we show that the $\cal{A}^*$ algorithm together with a standard bounding technique is superior to the well known Carillo-Lipman bounding since it excludes more nodes from consideration.

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Language(s): eng - English
 Dates: 1997
 Publication Status: Issued
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 Rev. Type: -
 Identifiers: Report Nr.: MPI-I-97-1-028
BibTex Citekey: LermenReinert97
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Title: Research Report / Max-Planck-Institut für Informatik
Source Genre: Series
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