Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree
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.
KeywordsMultiple Alignment Rooted Tree Pairwise Alignment Optimal Alignment Ancestral Sequence
Unable to display preview. Download preview PDF.
- 3.Myers, E.W., Miller, W.: Optimal alignments in linear space. Comput. Appl. Biosci. 4, 11–17 (1988)Google Scholar
- 6.Sankoff, D., Cedergren, R.J.: Simultaneous comparison of three or more sequences related by a tree. In: Sankoff, D., Kruskal, J.B. (eds.) Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison, pp. 253–264. Addison-Wesley, Reading (1983)Google Scholar
- 9.Hein, J.: A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6, 649–668 (1989)Google Scholar