Embedding strategies for effective use of information from multiple sequence alignments.

@article{Henikoff1997EmbeddingSF,
  title={Embedding strategies for effective use of information from multiple sequence alignments.},
  author={Steven Henikoff and Jorja G. Henikoff},
  journal={Protein science : a publication of the Protein Society},
  year={1997},
  volume={6 3},
  pages={698-705}
}
We describe a new strategy for utilizing multiple sequence alignment information to detect distant relationships in searches of sequence databases. A single sequence representing a protein family is enriched by replacing conserved regions with position-specific scoring matrices (PSSMs) or consensus residues derived from multiple alignments of family members. In comprehensive tests of these and other family representations, PSSM-embedded queries produced the best results overall when used with a… CONTINUE READING

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