Reticular alignment: A progressive corner-cutting method for multiple sequence alignment |
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| Authors: | Adrienn Szabó Ádám Novák István Miklós Jotun Hein |
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| Institution: | 1.Computer and Automation Research Institute,Hungarian Academy of Sciences,Budapest,Hungary;2.Faculty of Informatics,E?tv?s Loránd University,Budapest,Hungary;3.Department of Statistics,University of Oxford,Oxford,UK;4.Oxford Centre for Integrative Systems Biology,Department of Biochemistry,Oxford,UK;5.Alfréd Rényi Institute of Mathematics,Hungarian Academy of Sciences,Budapest,Hungary |
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| Abstract: | Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment.
Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead,
it defines a set of optimal and suboptimal alignments at each step during the progressive alignment. The set of alignments
are represented with a network to store them and use them during the progressive alignment in an efficient way. The program
contains a threshold parameter on which the size of the network depends. The larger the threshold parameter and thus the network,
the deeper the search in the alignment space for better scored alignments. |
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