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5.5 Bibliographic Notes

  1. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman: A basic local alignment search tool. Journal of Molecular Biology 215, 1990, pp. 403–410.

    Google Scholar 

  2. S. F. Altschul, T. L. Madden, A. Zhang, Z. Zhang, W. Miller, and D. J. Lipman: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 1997, 3389–3402.

    Article  Google Scholar 

  3. H. Carillo and D.J. Lipman: The multiple sequence alignment problem in biology. SIAM Journal on Applied Mathematics 48, 1988, pp. 1073–1082.

    Article  MathSciNet  Google Scholar 

  4. P. Clote and R. Backofen: Computational Molecular Biology — An Introduction. Wiley, 2000.

    Google Scholar 

  5. M. Dayhoff, R. M. Schwartz, and B. C. Orcutt: A model of evolutionary change in proteins. In: M. Dayhoff (ed.): Atlas of Protein Sequence and Structure Vol. 5, National Biomedical Research Foundation, 1978, pp. 345–352.

    Google Scholar 

  6. R. Durbin, S. Eddy, A. Krogh, and G. Mitchinson: Biological Sequence Analysis — Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.

    Google Scholar 

  7. W. J. Ewens and G. R. Grant: Statistical Methods in Bioinformatics — An Introduction. Springer, 2002.

    Google Scholar 

  8. D. Feng and R. Doolittle: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution 25, 1987, pp. 351–360.

    Article  Google Scholar 

  9. D. Gusfield: Efficient methods for multiple sequence alignment with guaranteed error bounds. Bulletin of Mathematical Biology 55, 1993, pp. 141–154.

    MATH  Google Scholar 

  10. D. Gusfield: Algorithms on Strings, Trees, and Sequences. Cambridge University Press, 1997.

    Google Scholar 

  11. A. Hansen: Bioinformatik — Ein Leitfaden für Naturwissenschaftler. Birkhäuser, 2001.

    Google Scholar 

  12. S. Henikoff and J. G. Henikoff: Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences of the U.S.A. 89, 1992, pp. 10915–10919.

    Article  Google Scholar 

  13. V. I. Levenshtein: Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics Doklady 6, 1966, pp. 707–710.

    MathSciNet  Google Scholar 

  14. M. Li, B. Ma, and L. Wang: Finding similar regions in many strings. Proceedings of the 31st ACM Annual Symposium on the Theory of Computing (STOC’99), 1999, pp. 473–482.

    Google Scholar 

  15. D. J. Lipman and W. R. Pearson: Rapid and sensitive protein similarity searches. Science 227, 1985, pp. 1435–1441.

    Article  Google Scholar 

  16. M. Middendorf: More on the complexity of common superstring and supersequence problems. Theoretical Computer Science 125(2), 1994, pp. 205–228.

    Article  MATH  MathSciNet  Google Scholar 

  17. S. B. Needleman, and C. D. Wunsch: A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48, 1970, pp. 443–453.

    Article  Google Scholar 

  18. W. R. Pearson: Flexible sequence similarity searching with the FASTA3 program package. Methods in Molecular Biology: Bioinformatics Methods and Protocols 132, 2000, pp. 185–219.

    Article  Google Scholar 

  19. W. R. Pearson and D. J. Lipman: Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the U.S.A. 85, 1988, pp. 2444–2448.

    Article  Google Scholar 

  20. P. A. Pevzner: Computational Molecular Biology — An Algorithmic Approach. MIT Press, 2000.

    Google Scholar 

  21. R. Rauhut: Bioinformatik: Sequenz — Struktur — Funktion. Wiley-VCH, 2001.

    Google Scholar 

  22. G. Schnitger: Algorithmen der Bioinformatik. Vorlesungsskript, Johann Wolfgang Goethe-Universität, Frankfurt am Main, 2001.

    Google Scholar 

  23. J. Setubal and J. Meidanis: Introduction to Computational Molecular Biology. PWS Publishing Company, 1997.

    Google Scholar 

  24. T. F. Smith and M. S. Waterman: Identification of common molecular subsequences. Journal of Molecular Biology 147, 1981, pp. 195–197.

    Article  Google Scholar 

  25. L. Wang and T. Jiang: On the complexity of multiple sequence alignment. Journal of Computational Biology 1(4), 1994, pp. 337–348.

    Article  Google Scholar 

  26. M. S. Waterman: Introduction to Computational Biology — Maps, Sequences and Genomes. Chapman & Hall/CRC, 1995.

    Google Scholar 

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(2007). Alignment Methods. In: Algorithmic Aspects of Bioinformatics. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71913-7_5

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  • DOI: https://doi.org/10.1007/978-3-540-71913-7_5

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