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Modeling Highly Repetitive Low-level Blast Exposure in Mice
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PSI-BLAST pseudocounts and the minimum description length principle.

Stephen F Altschul1, E Michael Gertz, Richa Agarwala

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov

Nucleic Acids Research
|December 18, 2008
PubMed
Summary

This study introduces the minimum description length principle to optimize pseudocounts in Position Specific Score Matrices (PSSMs) for improved protein sequence analysis. This method enhances PSI-BLAST

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Position Specific Score Matrices (PSSMs) are crucial for identifying distant protein sequence relationships.
  • The PSI-BLAST program uses pseudocounts in PSSMs, with the quantity being an empirical parameter.
  • Current methods lack a theoretical basis for selecting the number of pseudocounts.

Purpose of the Study:

  • To apply the minimum description length (MDL) principle for theoretically motivating pseudocount selection in PSSMs.
  • To enhance the accuracy of protein sequence similarity searches using PSI-BLAST.
  • To develop a data-driven approach for optimizing PSSM generation.

Main Methods:

  • Utilizing the minimum description length principle to determine pseudocount values.
  • Analyzing the relationship between pseudocounts, alignment size, and column conservation.
  • Implementing and evaluating a novel pseudocount calculation method within PSI-BLAST.

Main Results:

  • The MDL principle supports using a pseudocount number independent of alignment size for realistic datasets.
  • More conserved alignment columns should utilize fewer pseudocounts, increasing PSSM inter-column contrast.
  • A new pseudocount calculation method demonstrably improves PSI-BLAST retrieval accuracy.

Conclusions:

  • The minimum description length principle provides a robust theoretical framework for pseudocount selection in PSSMs.
  • Optimized pseudocounts lead to more sensitive and accurate protein sequence similarity searches.
  • The enhanced PSI-BLAST method, employing data-driven pseudocounts, is now the default for improved performance.