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

@article{Raphael2004ANM,
  title={A novel method for multiple alignment of sequences with repeated and shuffled elements.},
  author={Benjamin J. Raphael and Degui Zhi and Haixu Tang and Pavel A. Pevzner},
  journal={Genome research},
  year={2004},
  volume={14 11},
  pages={2336-46}
}
We describe ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences. The major difference between ABA and existing multiple alignment methods is that ABA represents an alignment as a directed graph, possibly containing cycles. This representation provides more flexibility than does a traditional alignment matrix or the recently introduced partial order alignment (POA) graph by allowing a larger class of evolutionary relationships between the aligned sequences. Our… CONTINUE READING

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