Position-based sequence weights

J Mol Biol. 1994 Nov 4;243(4):574-8. doi: 10.1016/0022-2836(94)90032-9.


Sequence weighting methods have been used to reduce redundancy and emphasize diversity in multiple sequence alignment and searching applications. Each of these methods is based on a notion of distance between a sequence and an ancestral or generalized sequence. We describe a different approach, which bases weights on the diversity observed at each position in the alignment, rather than on a sequence distance measure. These position-based weights make minimal assumptions, are simple to compute, and perform well in comprehensive evaluations.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Computer Simulation
  • Databases, Factual
  • Genetic Variation
  • Molecular Sequence Data
  • Sequence Alignment*