The value of position-specific scoring matrices for assessment of protein allegenicity

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12(Suppl 12):S21. doi: 10.1186/1471-2105-9-S12-S21.


Background: Bioinformatics tools are commonly used for assessing potential protein allergenicity. While these methods have achieved good accuracies for highly conserved sequences, they are less effective when the overall similarity is low. In this study, we assessed the feasibility of using position-specific scoring matrices as a basis for predicting potential allergenicity in proteins.

Results: Two simple methods for predicting potential allergenicity in proteins, based on general and group-specific allergen profiles, are presented. Testing results indicate that the performances of both methods are comparable to the best results of other methods. The group-specific profile approach, with a sensitivity of 84.04% and specificity of 96.52%, gives similar results as those obtained using the general profile approach (sensitivity = 82.45%, specificity = 96.92%).

Conclusion: We show that position-specific scoring matrices are highly promising for constructing computational models suitable for allergenicity assessment. These data suggest it may be possible to apply a targeted approach for allergenicity assessment based on the profiles of allergens of interest.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Allergens
  • Animals
  • Computational Biology / methods*
  • Databases, Factual
  • Databases, Protein
  • False Positive Reactions
  • Humans
  • Hypersensitivity, Immediate / diagnosis
  • Hypersensitivity, Immediate / immunology
  • Models, Statistical
  • Predictive Value of Tests
  • Proteins / chemistry*
  • Proteins / immunology*
  • Reproducibility of Results
  • Sequence Analysis, Protein
  • Software


  • Allergens
  • Proteins