PSI-BLAST pseudocounts and the minimum description length principle

  title={PSI-BLAST pseudocounts and the minimum description length principle},
  author={Stephen F. Altschul and E. Michael Gertz and Richa Agarwala and Alejandro A. Sch{\"a}ffer and Yi-Kuo Yu},
  booktitle={Nucleic acids research},
Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length… CONTINUE READING
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