1996, English, Article edition: Using substitution probabilities to improve position-specific scoring matrices Henikoff, Jorja G.; Henikoff, Steven

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  • text/​html
Published
  • Oxford University Press
  • 1996-04-01 00:00:00.0
Language
  • English

Edition details

Title
  • Using substitution probabilities to improve position-specific scoring matrices
Author
  • Henikoff, Jorja G.
  • Henikoff, Steven
Published
  • Oxford University Press
  • 1996-04-01 00:00:00.0
Physical Description
  • text/​html
Subjects
Notes
  • Each column of amino acids in a multiple alignment of protein sequences can be represented as a vector of 20 amino acid counts. For alignment and searching applications, the count vector is an imperfect representation of a position, because the observed sequences are an incomplete sample of the full set of related sequences. One general solution to this problem is to model unobserved sequences by adding artificial ‘pseudo-counts’ to the observed counts. We introduce a simple method for computing pseudo-counts that combines the diversity observed in each alignment position with amino acid substitution probabilities. In extensive empirical tests, this position-based method out-performed other pseudo-count methods and was a substantial improvement over the traditional average score method used for constructing profiles.
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  • Copyright (C) 1996, Oxford University Press
Language
  • English
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