Fundamentals of massive automatic pairwise alignments of protein sequences: Theoretical significance of Z-value statistics

Bioinformatics

Volumn 20, Issue 4, 2004, Pages 534-537

  Bastien, Olivier ^a,b   Aude, Jean Christophe ^c   Roy, Sylvaine ^a   Maréchal, Eric ^a  

^a CEA GRENOBLE   (France)

^b Gene IT   (France)

^c CEA SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CALCULATION; CLUSTER ANALYSIS; GENE CLUSTER; GENOME ANALYSIS; MONTE CARLO METHOD; NONHUMAN; PHYLOGENETIC TREE CONSTRUCTION METHOD; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROBABILITY; PROTEIN FUNCTION; RATING SCALE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS;

PLASMODIUM FALCIPARUM;

EID: 1542505031     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg440     Document Type: Article

References (26)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Arratia,R. and Waterman,M.S. (1994) A phase transition for the score in matching random sequences allowing deletions. Ann. Appl. Prob., 4, 200-225.
3. Aude,J.C. and Louis,A. (2002) An incremental algorithm for Z-value computations. Comput. Chem., 26, 403-411.
4. Bacro,J.-N. and Comet,J.-P. (2001) Sequence alignment: An approximation law for the Z-value with applications to databank scanning. Comput. Chem., 25, 401-410.
5. Bienaymé,I.J. (1853) Considérations a l'appui de la découverte de Laplace sur la loi de probabilité dans la méthode des moindres carrés. C.R. Acad. Sci. Paris, 37, 309-324.
6. Brocchieri,L. (2001) Low-complexity regions in Plasmodium proteins: In search of a function. Genome Res., 11, 195-197.
7. Chebyshev,P.L. (1867) Des valeurs moyennes. Liouville's J. Math. Pures. Appl., 12, 177-184.
8. Codani,J.J., Comet,J.P., Aude,J.C., Glémet,E., Wozniak,A., Risler,J.L., Hénaut,A. and Slonimski,P.P. (1999) Automatic analysis of large-scale pairwise alignments of protein sequences. Methods Microbiol., 28, 229-244.
9. Comet,J.P., Aude,J.C., Glémet,E., Risler,J.L., Hénaut,A., Slonimski,P.P. and Codani,J.J. (1999) Significance of Z-value statistics of Smith-Waterman scores for protein alignments. Comput. Chem., 23, 317-331.
10. Dardel,F. and Képès,F. (2002) Bioinformatique: Génomique et Post-Génomique. Les éditions de l'école polytechnique edit, Paris.
11. Doolittle,R.F. (1981) Similar amino acid sequences: Chance or common ancestry? Science, 214, 149-159.
12. Fitch,W.M. (1983) Random sequences. J. Mol. Biol., 163, 171-176.
13. Gardner,M.J., Hall,N., Fung,E., White,O., Berriman,M., Hyman,R.W., Carlton,J.M., Pain,A., Nelson,K.E., Bowman,S. et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419, 498-511.
14. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci., USA, 87, 2264-2268.
15. Lipman,D.J. and Pearson,W.R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.
16. Mott,R. and Tribe,R. (1999) Approximate statistics of gapped alignment. J. Comput. Biol., 6, 91-112.
17. Musto,H., Rodriguez-Maseda,H. and Bernardi,G. (1995) Compositional properties of nuclear genes from Plasmodium falciparum. Gene, 152, 127-132.
18. Nishizawa,M. and Nishizawa,K. (1998) Biased usages of arginines and lysines in proteins are correlated with local-scale fluctuations of the G + C content of DNA sequences. J. Mol. Evol., 47, 385-393.
19. Nishizawa,K., Nishizawa,M. and Kim,K.S. (1999) Tendency for local repetitiveness in amino acid usages in modern proteins. J. Mol. Biol., 294, 937-953.
20. Pizzi,E. and Frontali,C. (1999) Molecular evolution of coding and non-coding regions in Plasmodium. Parassitologia, 41, 89-91.
21. Pizzi,E. and Frontali,C. (2001) Low-complexity regions in Plasmodium falciparum proteins. Genome Res., 11, 218-229.
22. Singer,G.A. and Hickey,D.A. (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol., 17, 1581-1588.
23. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
24. Waterman,M.S. (1994) Estimating of statistical significance of sequence alignment. Philos. Trans. R. Soc. Lond., 344, 383-390.
25. Waterman,M.S. and Vingron,M. (1994a) Sequence comparison significance and Poisson approximation. Stat. Sci., 9, 367-381.
26. Waterman,M.S. and Vingron,M. (1994b) Rapid and accurate estimates of statistical significance for sequence data base searches. Proc. Natl Acad. Sci., USA, 91, 4625-4628.