Journal of Molecular Evolution

, Volume 45, Issue 1, pp 50–59

Analysis of donor splice sites in different eukaryotic organisms

  • Igor B. Rogozin
  • Luciano Milanesi

DOI: 10.1007/PL00006200

Cite this article as:
Rogozin, I.B. & Milanesi, L. J Mol Evol (1997) 45: 50. doi:10.1007/PL00006200


We present here a new algorithm for functional site analysis. It is based on four main assumptions: each variation of nucleotide composition makes a different contribution to the overall binding free energy of interaction between a functional site and another molecule; nonfunctioning site-like regions (pseudosites) are absent or rare in genomes; there may be errors in the sample of sites; and nucleotides of different site positions are considered to be mutually dependent. In this algorithm, the site set is divided into subsets, each described by a certain consensus. Donor splice sites of the human protein-coding genes were analyzed. Comparing the results with other methods of donor splice site prediction has demonstrated a more accurate prediction of consensus sequences AG/GU(A,G), G/GUnAG, /GU(A,G)AG, /GU(A,G)nGU, and G/GUA than is achieved by weight matrix and consensus (A,C)AG/GU(A,G)AGU with mismatches. The probability of the first type error, El, for the obtained consensus set was about 0.05, and the probability of the second type error, E2, was 0.15. The analysis demonstrated that accuracy of the functional site prediction could be improved if one takes into account correlations between the site positions. The accuracy of prediction by using human consensus sequences was tested on sequences from different organisms. Some differences in consensus sequences for the plant Arabidopsis sp., the invertebrate Caenorhabditis sp., and the fungus Aspergillus sp. were revealed. For the yeast Saccharomyces sp. only one conservative consensus, /GUA(U,A,C)G(U,A,C), was revealed (El = 0.03, E2 = 0.03). Yeast is a very interesting model to use for analysis of molecular mechanisms of splicing.

Key words

Donor splice site Classification Accuracy Correlating positions Functional site 

Copyright information

© Springer-Verlag New York Inc 1997

Authors and Affiliations

  • Igor B. Rogozin
    • 1
  • Luciano Milanesi
    • 1
  1. 1.Istituto di Tecnologie Biomediche AvanzateConsiglio Nazionale Delle RicercheMilanoItaly

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