Recent progress in multiple sequence alignment: A survey

Pharmacogenomics

Volumn 3, Issue 1, 2002, Pages 131-144

  Notredame, Cédric ^a  

^a CNRS Aix Marseille University   (France)

Author keywords

BLAST; Hidden Markov model; Multiple sequence alignment; T Coffee

Indexed keywords

ALGORITHM; ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; METHODOLOGY; PHYLOGENY; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STOCHASTIC MODEL; STRUCTURE ANALYSIS;

ALGORITHMS; PHYLOGENY; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

EID: 0036208872     PISSN: 14622416     EISSN: None     Source Type: Journal    
DOI: 10.1517/14622416.3.1.131     Document Type: Article

References (84)

1. Basic local alignment search tool
2. PHD - An automatic server for protein secondary structure prediction
3. The neighbor-joining method: A new method for reconstructing phylogenetic trees
4. Maximum likelihood methods
5. Confidence limits on phylogenies: An approach using the bootstrap
6. The PROSITE database its status in
7. PRINTS-S: The database formerly known as PRINTS
8. Profile analysis
9. Protein modeling using hidden markov models: Analysis of globins
10. Improving the sensitivity of the sequence profile method
11. The Pfam protein families database
12. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
13. GOR method for predicting protein secondary structure from amino acid sequence
14. Protein secondary structure prediction based on position-specific scoring matrices
15. Review: Protein secondary structure prediction continues to rise
16. Correlated mutations and residue contacts in proteins
17. Comparative anatomy of 16S-like ribosomal RNA
18. Multiple DNA and protein sequence based on segment-to-segment comparison
19. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
20. Match-Box server: A multiple sequence alignment tool placing emphasis on reliability
21. A workbench for multiple alignment construction and analysis
22. Playing with blocks: Some pitfalls of forcing multiple alignments
23. Statistical methods and insight for protein and DNA sequences
24. Trees stars and multiple biological sequence alignment
25. Weights for data related by a tree
26. A model of evolutionary change in proteins. Detecting distant relationships: Computer methods and results
27. Sequence alignment and penalty choice
28. A tool for multiple sequence alignment
29. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice
30. Further improvement in methods of group-to-group sequence alignment with generalized profile operations
31. A comprehensive comparison of multiple sequence alignment programs
32. Evaluation measures of multiple sequence alignments
33. DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
34. T-Coffee: A novel algorithm for multiple sequence alignment
35. Hidden Markov models of biological primary sequence information
36. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set
37. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
38. On the complexity of multiple sequence alignment
39. DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment
40. Clustal: A package for performing multiple sequence alignment on a microcomputer
41. Multiple sequence alignment with hierarchical clustering
42. The alignment of sets of sequences and the construction of phylogenetic trees. An integrated method
43. Progressive sequence alignment as a prerequisite to correct phylogenetic trees
44. A flexible method to align large numbers of biological sequences
45. A general method applicable to the search for similarities in the amino acid sequence of two proteins
46. A strategy for the rapid multiple alignment of protein sequences: Confidence levels from tertiary structure comparisons
47. Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinements as Assessed by Reference to Structural Alignments
48. Two strategies for sequence comparison: Profile-preprocessed and secondary structure-induced multiple alignment
49. Hidden Markov Models in Computational Biology: Applications to Protein Modeling
50. Multiple Sequence Alignment using Simulated Annealing
51. SAGA: Sequence alignment by genetic algorithm
52. A genetic algorithm for multiple molecular sequence alignment
53. Multiple sequence alignment using parallel genetic algorithms
54. Multiple protein sequence comparison by genetic algorithms
55. Multiple sequence alignment using evolutionary programming
56. Evolutionary computation techniques for multiple sequence alignment
57. Multiple Alignment for Structural Functional or phylogenetic analyses of Homologous Sequences
58. GCG package
59. The multiple sequence alignment problem in biology
60. An iterative method for faster sum-of-pair multiple sequence alignment
61. Equation of state calculations by fast computing machines
62. Adaptation in natural and artificial systems
63. Multiple sequence alignment by parallel simulated annealing
64. Genetic Algorithms
65. COFFEE: An objective function for multiple sequence alignments
66. RAGA: RNA sequence alignment by genetic algorithm
67. Multiple alignment using hidden Markov models
68. A novel randomized iterative strategy for aligning multiple protein sequences
69. Asymetric-iterated multiple alignment of protein sequences
70. The maximum weight trace problem in multiple sequence alignment
71. Motif recognition and alignment for many sequences by comparison of dot-matrices
72. DIALIGN: Finding local similarities by multiple sequence alignment
73. A time-efficient linear-space local similarity algorithm
74. Combining many multiple alignments in one improved alignment
75. An exact solution for the segment-to-segment multiple sequence alignment problem
76. An approach to improving multiple alignments of protein sequences using predicted secondary structure
77. A fully automatic evolutionary classification of protein folds: Dali domain dictionary version 3
78. Multiple protein sequence alignment using double-dynamic programming
79. A rapid method of protein structure alignment
80. Structure comparison and structure patterns
81. Mocca: Semi-automatic method for domain hunting
82. A method to recognize distant repeats in protein sequences
83. Hidden Markov models for sequence analysis: Extension and analysis of the basic method