Phylogenetic information improves homology detection.

@article{Rehmsmeier2001PhylogeneticII,
  title={Phylogenetic information improves homology detection.},
  author={Marc Rehmsmeier and Martin Vingron},
  journal={Proteins},
  year={2001},
  volume={45 4},
  pages={360-71}
}
We present a database search method that is based on phylogenetic trees (treesearch). The method is used to search a protein sequence database for homologs to a protein family. In preparation for the search, a phylogenetic tree is constructed from a given multiple alignment of the family. During the search, each database sequence is temporarily inserted into the tree, thus adding a new edge to the tree. Homology between family and sequence is then judged from the length of this edge. In a… CONTINUE READING