The estimation of statistical parameters for local alignment score distributions

Nucleic Acids Research

Volumn 29, Issue 2, 2001, Pages 351-361

  Altschul, Stephen F ^a   Bundschuh, Ralf ^b   Olsen, Rolf ^b   Hwa, Terence ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; CURVE FITTING; GENETIC PROCEDURES; PRIORITY JOURNAL; SCORING SYSTEM; STATISTICAL PARAMETERS; TECHNIQUE;

EID: 0035863762     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.2.351     Document Type: Article

References (38)

1. Improved tools for biological sequence comparison
2. Basic local alignment search tool
3. Identification of protein coding regions by database similarity search
4. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
5. Identification of common molecular subsequences
6. Pattern recognition in genetic sequences by mismatch density
7. Phase transitions in sequence matches and nucleic acid structure
8. A phase transition for the score in matching random sequences allowing deletions
9. Critical phenomena for sequence matching with scoring
10. Sequence alignment and penalty choice. Review of concepts, case studies and implications
11. Rapid assessment of extremal statistics for grapped local alignment
12. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
13. Limit distribution of maximal non-aligned two-sequence segmental score
14. The statistical distribution of nucleic acid similarities
15. The significance of protein sequence similarities
16. Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores
17. Rapid and accurate estimates of statistical significance for sequence database searches
18. Sequence comparison significance and Poisson approximation
19. Local alignment statistics
20. Empirical statistical estimates for sequence similarity searches
21. Accurate formula for P-values of gapped local sequence and profile alignments
22. Locally optimal subalignments using nonlinear similarity functions
23. A new algorithm for best subsequence alignments with applications to tRNA-rRNA comparisons
24. Distribution of glutamine and asparagine residues and their near neighbors in peptides and proteins
25. Amino acid substitution matrices from protein blocks
26. An improved algorithm for matching biological sequences
27. Optimal sequence alignments
28. Optimal sequence alignment using affine gap costs
29. Optimal alignments in linear space
30. Amino acid substitution matrices from an information theoretic perspective
31. Strong limit theorems of empirical functionals for large exceedances of partial sums of i.i.d. variables
32. IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
33. An extreme value theory for sequence matching
34. A model of evolutionary change in proteins
35. Matrices for detecting distant relationships