SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models

@article{Edgar2003SATCHMOSA,
  title={SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models},
  author={Robert C. Edgar and Kimmen Sj{\"o}lander},
  journal={Bioinformatics},
  year={2003},
  volume={19 11},
  pages={1404-11}
}
MOTIVATION Aligning multiple proteins based on sequence information alone is challenging if sequence identity is low or there is a significant degree of structural divergence. We present a novel algorithm (SATCHMO) that is designed to address this challenge. SATCHMO simultaneously constructs a tree and a set of multiple sequence alignments, one for each internal node of the tree. The alignment at a given node contains all sequences within its sub-tree, and predicts which positions in those… CONTINUE READING
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