A novel method for multiple alignment of sequences with repeated and shuffled elements

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Figure 1.
Figure 1.

An alignment is a mapping from a set of input sequences to a directed graph. Positions that map to the same vertex are aligned. Standard MSA programs map each sequence to a single path. Each vertex on the path contains either a letter or a gap character from each sequence. POA maps each sequence to a DAG. The structure of the DAG permits alignments where a subset of the sequences is aligned at a position.

This Article

  1. Genome Res. 14: 2336-2346

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