Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions.

@article{Stojanovic1999ComparisonOF,
  title={Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions.},
  author={Nikola Stojanovic and Liliana Florea and Cathy Riemer and Deborah L Gumucio and Jerry Laverne Slightom and Morris Goodman and Webb Miller and Ross C. Hardison},
  journal={Nucleic acids research},
  year={1999},
  volume={27 19},
  pages={
          3899-910
        }
}
Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily for DNA sequences. Two of the methods are already in common use; these are based on good column agreement and high information content. Three additional methods find blocks with… CONTINUE READING

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