Exact and Asymptotic Distribution of the Local Score of One i.i.d. Random Sequence

  • Sabine Mercier
  • Dominique Cellier
  • François Charlot
  • Jean-Jacques Daudin
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2066)


We propose two new and complementary methods to assess the statistical significance of high scoring segments, within both long and short sequences. The numerical results show that these methods improve the work of Karlin et al. implemented in BLAST for the comparison of two sequences.


local score statistical significance sequence analysis 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Altschul, S., Gish, W., Miller, W. Myers, E., Lipman, D.: Basic Local Alignment Search Tool. J. Mol. Biol. 215 (1990), 403–410Google Scholar
  2. 2.
    Daudin, J.-J., Mercier, S.: Distribution exacte d’une suite de variables indépendantes et identiquement distribuées. C. R. Acad. Sci. Paris tome 329 série I (1999) 815–820zbMATHMathSciNetGoogle Scholar
  3. 3.
    Dayhoff, M., Schwartz, R., Orcutt, B.: A model of evolutionary change in protein. Atlas of Protein Sequences and Structure, 5 (1978), 345–352Google Scholar
  4. 4.
    Dembo, A., Karlin, S., Zeitouni, O.: Limit distribution of maximal non-aligned two-sequences segmental score. Ann. Prob. 22 (1994) 2022–2039zbMATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Karlin, S., Altschul, S.F.: Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87 (1990) 2264–2268zbMATHCrossRefGoogle Scholar
  6. 6.
    Karlin, S., Dembo, A.: Limit distributions of maximal segmental score among Markov-dependent partial sums. Adv. Appl. Prob. 24 (1992) 113–140zbMATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Karlin, S., Dembo, A., Kawabata, T.: Statistical composition of high-scoring segments from molecular sequences. Ann. Statist. 18 (1990) 571–581zbMATHCrossRefMathSciNetGoogle Scholar
  8. 8.
    Mercier, S.: Statistiques des scores pour l’analyse et la comparaison de séquences biologiques. Thèse, Université de Rouen (1999)Google Scholar
  9. 9.
    Mercier, S., Daudin, J.-J.: Exact distribution for the local score of one i.i.d. random sequence. To appear in J. Comp. Biol.Google Scholar
  10. 10.
    Mott, R., Tribes, R.: Approximate Statistics of Gapped Alignments. J. Comp. Biol. 6 1 (1999) 91–112CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Sabine Mercier
    • 1
  • Dominique Cellier
    • 2
  • François Charlot
    • 2
  • Jean-Jacques Daudin
    • 3
  1. 1.UFR SES, Département Mathématique et InformatiqueUniversité de Toulouse IIFrance
  2. 2.Analyse et Modèles Stochastiques UPRES A 6085Université de RouenFrance
  3. 3.Département OMIP, UMR INAPG-INRA 96021111Institut National Agronomique Paris-GrignonFrance

Personalised recommendations