Abstract
Many methods in bioinformatics rely on evolutionary relationships between protein, DNA, or RNA sequences. Alignment is a crucial first step in most analyses, since it yields information about which regions of the sequences are related to each other. Here, a new method for multiple parsimony alignment over a tree is presented. The novelty is that an affine gap cost is used rather than a simple linear gap cost. Affine gap costs have been used with great success for pairwise alignments and should prove useful in the multiple alignment scenario. The algorithmic challenge of using an affine gap cost in multiple alignment is the introduction of dependence between different columns in the alignment. The utility of the new method is illustrated by a number of protein sequences where increased alignment accuracy is obtained by using multiple sequences.
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Knudsen, B. (2003). Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree. In: Benson, G., Page, R.D.M. (eds) Algorithms in Bioinformatics. WABI 2003. Lecture Notes in Computer Science(), vol 2812. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39763-2_31
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DOI: https://doi.org/10.1007/978-3-540-39763-2_31
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-20076-5
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