Optimal sequence alignments.

@article{Fitch1983OptimalSA,
  title={Optimal sequence alignments.},
  author={Walter M. Fitch and Temple F. Smith},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={1983},
  volume={80 5},
  pages={1382-6}
}
Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment between a set of codons for the chicken alpha- and beta-hemoglobin sequence when it is in fact discoverable by a more general treatment of gaps. Fundamental reasons for this are discussed. 

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