CS 5124: Algorithms in Bioinformatics

Fall Semester, 2003
Resourses on the FASTA (Fast Alignment) Package

Papers on FASTA, Chronologically

  1. Lipman, D. J. and Pearson, W. R. (1985)
    Rapid and sensitive protein similarity searches
    Science 227, 1435-1441.

  2. Pearson, W. R. and Lipman, D. J. (1988)
    Improved tools for biological sequence comparison
    Proc. Natl. Acad. Sci. USA 85, 2444-2448.

  3. W. R. Pearson (1991)
    Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.
    Genomics 11, pp. 635-650.

  4. Chao, K.-M., Pearson, W. R., and Miller, W. (1992)
    Aligning two sequences within a specified diagonal band
    Comp. Appl. Biosci. 8, 481-487.

  5. W. R. Pearson (1994)
    Using the FASTA program to search protein and DNA sequence databases
    Methods Mol. Biol. 24, pp. 307-331.

  6. W. R. Pearson (1994)
    Using the FASTA program to search protein and DNA sequence databases
    Methods Mol. Biol. 25, pp. 365-389.

  7. Pearson, W. R. (1995)
    Comparison of methods for searching protein sequence databases
    Protein Sci. 4, 1145-1160.

  8. Pearson, W. R. (1996)
    Effective protein sequence comparison
    Methods Enzymol. 266, 227- 258.

  9. William R. Pearson, Todd Wood, Zheng Zhang, and Webb Miller (1997)
    Comparison of DNA sequences with protein sequences
    Genomics 46, pp. 24-36.

  10. Pearson, W. R. (1997)
    Identifying distantly related protein sequences
    Comput. Appl. Biosci. 13, 325-332.

  11. Pearson, W. R. (1998)
    Empirical statistical estimates for sequence similarity searches
    J. Mol. Biol. 276, 71-84.

  12. T. C. Wood and W. R. Pearson (1999)
    Evolution of protein sequences and structures
    J. Mol. Biol. 291:977-995.

  13. Pearson, W. R. (2000)
    Flexible sequence similarity searching with the FASTA3 program package
    Methods Mol. Biol. 132:185-219.

  14. W. R. Pearson and T. C. Wood (2001)
    "Statistical significance in biological sequence comparison"
    in Handbook of Statistical Genetics, D. J. Balding, M. Bishop, and C. Cannings eds.
    London: Wiley, pp. 39-65.

Internet Resources for FASTA

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