Contextual alignment of biological sequences (Extended abstract)

Bioinformatics

Volumn 18, Issue SUPPL. 2, 2002, Pages

  Gambin, Anna ^a   Lasota, Sławomir ^a   Szklarczyk, Radosław ^a   Tiuryn, Jerzy ^a   Tyszkiewicz, Jerzy ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; CONFERENCE PAPER; COST; DNA SEQUENCE; GENE SEQUENCE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PRIORITY JOURNAL;

EID: 12144279008     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.suppl_2.S116     Document Type: Conference Paper

References (18)

1. Comet,J.P., Aude,J.C., Glemet,E., Henaut,J.L., 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.
2. Durbin,R., Eddy,S.R., Krogh,A. and Mitchison,G. (1998) Biological sequence analysis, Probabilistic models of proteins and nucleid acids, Cambridge University Press.
3. Dayhoff,M.O., Schwartz,R.M. and Orcutt,B.C. (1978) A model of evolutionary change in proteins. In Dayhoff,M.O. (ed.), Atlas of Protein Sequence and Structure. 5, pp. 345-352.
4. Gusfield,D. (1997) Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press.
5. Gambin,A., Lasota,S., Szklarczyk,R., Tiuryn,J. and Tyszkiewicz,J. (2002a) Contextual alignment of biological sequences. Currents in Computational Molecular Biology. Posters from RECOMB 2002.
6. Gambin,A. and Tyszkiewicz,J. (2002b) Substitution matrices for contextual alignment. In Nicolas,J. and Thermes,C. (eds), Journees Ouvertes Biologie Informatique Mathematique (JOBIM 2002). pp. 227-238.
7. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
8. Ioerger,T.R. (1997) The context-dependence of amino acid properties. Intelligent Systems in Molecular Biology. AAAI Press, pp. 157-166.
9. Jensen,J.L. and Pedersen,A.M.K (2000) Probabilistic models of DNA sequence evolution with context dependent rates of substitution. Advances in Applied Probability, 32, 499-517.
10. Schulz,G. and Schirmer,R. (1979) Principles of Protein Structure. Springer, New York.
11. Stryer,L. (1995) Biochemistry. W.H. Freeman and Company.
12. Schöniger,M. and von Haeseler,A. (1994) A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol., 3, 240-247.
13. Smith,T.F. and Waterman,M.S. (1981) The identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
14. Tavaré,S. and Giddings,B.W. (1989) Some statistical aspects of the primary structure of nucleotide sequences. In Waterman,M.S. (ed.), Mathematical methods for DNA sequences. pp. 117-132.
15. von Haeseler,A. and Schöniger,M. (1998) Evolution of DNA or amino acid sequences with dependent sites. J. Comput. Biol., 5, 149-163.
16. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
17. Vingron,M. and Waterman,M.S. (1995) Statistical significance of local alignments with gaps. Bioinformatics: from Nucleid Acids and Proteins to Cell Methabolism. pp. 75-84.
18. Wilbur,W.J. and Lipman,D.J. (1984) The context dependent comparison of biological sequences. SIAM J. Appl. Math., 44, 557-567.