Aligning amino acid sequences: Comparison of commonly used methods

  title={Aligning amino acid sequences: Comparison of commonly used methods},
  author={Da Fei Feng and Mark S. Johnson and Russell F. Doolittle},
  journal={Journal of Molecular Evolution},
We examined two extensive families of protein sequences using four different alignment schemes that employ various degrees of “weighting” in order to determine which approach is most sensitive in establishing relationships. All alignments used a similarity approach based on a general algorithm devised by Needleman and Wunsch. The approaches included a simple program, UM (unitary matrix), whereby only identities are scored; a scheme in which the genetic code is used as a basis for weighting (GC… CONTINUE READING


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