CS 5124: Algorithms in Bioinformatics

Fall Semester, 2004
Papers Analyzing Sequence Statistics and Algorithms

The Statistics of Sequence Similarity Scores at NCBI
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Papers on Sequence Analysis, Chronologically

1. Samuel Karlin and Stephen F. Altschul (1990)
   Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
   Proc Natl Acad Sci U S A 87, pp. 2264-2268.

2. Steven Henikoff and Jorja G. Henikoff (1992)
   Amino acid substitution matrices from protein blocks
   Proc Natl Acad Sci U S A 89, pp. 10915-10919.

3. Samuel Karlin and Stephen F. Altschul (1993)
   Applications and statistics for multiple high-scoring segments in molecular sequences
   Proc Natl Acad Sci U S A 90, pp. 5873-5877.

4. A. Dembo, S. Karlin, and O. Zeitouni (1994)
   Limit distribution of maximal non-aligned two-sequence segmental score
   Annals of Probability 22, pp. 2022-2039.

5. E. G. Shpaer, M. Robinson, D. Yee, J. D. Candlin, R. Mines, and T. Hunkapiller (1996)
   Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA
   Genomics 38, pp. 179-191.

6. Jinghui Zhang and Thomas L. Madden (1997)
   PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation
   Genome Research 7, pp. 649-656.

7. Zheng Zhang, Alejandro A. Schäffer, Webb Miller, Thomas L. Madden, David J. Lipman, Eugene V. Koonin and Stephen F. Altschul (1998)
   Protein sequence similarity searches using patterns as seeds
   Nucleic Acids Research 26, pp. 3986-3990.

8. Pankaj Agarwal and David J. States (1998)
   Comparative accuracy of methods for protein sequence similarity search
   Bioinformatics 14, pp. 40-47.

9. R. Spang and M. Vingron (1998)
   Statistics of large-scale sequence searching.
   Bioinformatics 14, pp. 279-284.

10. I. Anderson and A. Brass (1998)
    Searching DNA databases for similarities to DNA sequences: when is a match significant?
    Bioinformatics 14, pp. 349-356.

11. Murvai J, Vlahovicek K, Barta E, Parthasarathy S, Hegyi H, Pfeiffer F, and Pongor S. (1999)
    The domain-server: direct prediction of protein domain-homologies from BLAST search
    Bioinformatics 15, pp. 343-344.

12. Scott C.-H. Pegg and Patricia C. Babbitt (1999)
    Shotgun: getting more from sequence similarity searches
    Bioinformatics 15, pp. 729-740.

13. Yuri I. Wolf, Steven E. Brenner, Paul A. Bash, and Eugene V. Koonin (1999)
    Distribution of Protein Folds in the Three Superkingdoms of Life
    Genome Research 9, pp. 17-26.

14. Murvai J, Vlahovicek K, Pongor S. (2000)
    A simple probabilistic scoring method for protein domain identification
    Bioinformatics 16, pp. 1155-1156.

15. Webber C, Barton GJ (2001)
    Estimation of P-values for global alignments of protein sequences
    Bioinformatics 17, pp. 1158-1167.

16. Golan Yona and Michael Levitt (2001)
    Within the Twilight Zone: A Sensitive Profile-Profile Comparison Tool Based on Information Theory
    Journal of Molecular Biology 315, pp. 1257-1275.

17. R. Spang and Martin Vingron (2001)
    Limits of homology detection by pairwise sequence comparison
    Bioinformatics 17, pp. 338-342.

18. Bin Ma, John Tromp, and Ming Li (2002)
    PatternHunter: faster and more sensitive homology search
    Bioinformatics 18, pp. 440-445.

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