Accurate formula for P-values of gapped local sequence and profile alignments

Journal of Molecular Biology

Volumn 300, Issue 3, 2000, Pages 649-659

  Mott, R ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Protein profile; Protein sequence; Sequence alignment; Statistical significance

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DATA BASE; GENETIC PROCEDURES; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS;

EID: 0034647416     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3875     Document Type: Article

References (37)

1. Local alignment statistics
2. Basic local alignment search tool
3. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
4. Stochastic scrabble: Large deviations for sequences with scores
5. Pfam 3.1: 1313 multiple alignments match the majority of proteins
6. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
7. Significance of protein sequence similarities
8. A statistical theory of sequence alignment with gaps
9. Profile hidden Markov models
10. Multiple-alignment and sequence searches
11. An improved algorithm for matching biological sequences
12. Profile analysis: Detection of distantly related proteins
13. Statistical studies of biomolecular sequences: Score-based methods
14. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
15. Applications and statistics for multiple high-scoring segments in molecular sequences
16. Limit distributions of maximal segmental score amongst Markov-dependent partial sums
17. Hidden Markov models for detecting remote protein homologues
18. Bayesian inference on biopolymer models
19. Sequence Comparisons with Concave Weighting Functions
20. Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores
21. Local sequence alignments with monotonic gap penalties
22. Approximate statistics of gapped alignments
23. SCOP: A structural classification of proteins database for the investigation of sequences and structures
24. Rapid asessment of extremal statistics for gapped local alignment
25. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
26. Empirical statistical estimates for sequence similarity searches
27. Improved tools for biological sequence comparison
28. Distribution of glutamine and asparagine residues and their near neighbors in peptides and proteins
29. Software to match a protein sequence againts a collection of PSI-BLAST-constructed position-specific score matrices
30. SMART, a simple modular architecture research tool: Identification of signalling domains
31. Identification of common molecular subsequences
32. Statistics of large-scale sequence searching
33. Rapid and accurate estimates of statistical significance for sequence database searches
34. Sequence comparison significance and poisson approximation
35. Phase transitions in sequence matches and nucleic acid structure