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Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree

  • Bjarne Knudsen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)

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.

Keywords

Multiple Alignment Rooted Tree Pairwise Alignment Optimal Alignment Ancestral Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Bjarne Knudsen
    • 1
  1. 1.Department of ZoologyUniversity of FloridaGainesvilleUSA

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