Pairwise Sequence Alignment

@inproceedings{WheelerVersion2007PairwiseSA,
  title={Pairwise Sequence Alignment},
  author={David WheelerVersion},
  year={2007}
}
Only alignment of homologous sequences seems meaningful as it is unclear what an alignment of non-homologous sequences means. So as viewed here, an alignment is a partial reconstruction of the path of molecular evolution. Solving ii. above is highly motivating for a molecular biologist. The moment a new molecule A is found to be homologous to an old well studied molecule B, much of the knowledge of B probably is true for A as well. This is because function and structure evolves much slower than… 
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