Multiple alignment of complete sequences (MACS) in the post-genomic era

Gene

Volumn 270, Issue 1-2, 2001, Pages 17-30

  Lecompte, Odile ^a   Thompson, Julie D ^a   Plewniak, Frédéric ^a   Thierry, Jean Claude ^a   Poch, Olivier ^a  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Bioinformatics; Functional genomics; Genome annotation; Sequence analysis

Indexed keywords

DNA; PROTEIN; RNA;

AMINO ACID SEQUENCE; COMPARATIVE STUDY; DATA BASE; GENOME; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; RELIABILITY; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VALIDATION PROCESS;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0035972742     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(01)00461-9     Document Type: Review

References (137)

1. Ubiquitous distributed objects with CORBA
2. Alignment algorithm for homology modelling and threading
3. Basic local alignment search tool
4. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
5. Position-specific annotation of protein function based on multiple homologs
6. Automated genome sequence analysis and annotation
7. Sequence alignment in molecular biology
8. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
9. Lineage-specific loss and divergence of functionally linked genes in eukaryotes
10. Homology modelling by distance geometry
11. PRINTS-S: The database formerly known as PRINTS
12. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons
13. The Pfam protein families database
14. ORBIT: An integrated environment for user-customized bioinformatics tools
15. Dealing with database explosion: A cautionary note
16. Applicability of the multiple alignment algorithm for detection of weak patterns: Periodically distributed DNA pattern as a study case
17. Go hunting in sequence databases but watch out for the traps
18. Genome and proteome informatics
19. Predicting functions from protein sequences-where are the bottlenecks?
20. Errors in genome annotation
21. Target selection for structural genomics
22. Expectations from structural genomics
23. A symmetric-iterated multiple alignment of protein sequences
24. Combining many multiple alignments in one improved alignment
25. An overview of structural genomics
26. The multiple sequence alignment problem in biology
27. A method to predict functional residues in proteins
28. Kleisli: A new tool for data integration in biology
29. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
30. Application of multiple sequence alignment profiles to improve protein secondary structure prediction
31. Re-annotating the mycoplasma pneumoniae genome sequence: Adding value, function and reading frames
32. Improving protein secondary structure prediction with aligned homologous sequences
33. Protein annotation: Detective work for function prediction
34. Multiple alignment using hidden Markov models
35. Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
36. Assessing evolutionary relationships among microbes from whole-genome analysis
37. Protein function in the post-genomic era
38. Progressive sequence alignment as a prerequisite to correct phylogenetic trees
39. Distinguishing homologous from analogous proteins
40. The future of protein secondary structure prediction accuracy
41. Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture
42. Who's your neighbor? New computational approaches for functional genomics
43. Orthologs, paralogs and genome comparisons
44. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
45. Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment
46. Genomics: From novel genes to new therapeutics in parasitology
47. Recurring local sequence motifs in proteins
48. Analysis and prediction of functional sub-types from protein sequence alignments
49. Unified approach to alignment and phylogenies
50. Increased coverage of protein families with the blocks database servers
51. Gene families: The taxonomy of protein paralogs and chimeras
52. Mycoplasma pneumoniae and Mycoplasma genitalium: A comparison of two closely related bacterial species
53. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium
54. The GeneQuiz web server: Protein functional analysis through the Web
55. The PROSITE database, its status in 1999
56. The FSSP database: Fold classification based on structure-structure alignment of proteins
57. Protein folds and families: Sequence and structure alignments
58. Evolution of simple sequence in proteins
59. Multiple sequence alignment by parallel simulated annealing
60. Key residues approach to the definition of protein families and analysis of sparse family signatures
61. Horizontal gene transfer among genomes: The complexity hypothesis
62. Alfresco-a workbench for comparative genomic sequence analysis
63. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
64. Comparative genomes of Chlamydia pneumoniae and C. trachomatis
65. What we do not know about sequence analysis and sequence databases
66. Hidden Markov models for detecting remote protein homologies
67. Enhanced genome annotation using structural profiles in the program 3D- PSSM
68. Alignment of possible secondary structures in multiple RNA sequences using simulated annealing
69. The impact of comparative genomics on our understanding of evolution
70. Initial sequencing and analysis of the human genome. International human genome sequencing consortium
71. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
72. Genome evolution at the genus level: Comparison of three complete genomes of hyperthermophilic Archaea
73. Chemical ligands, genomics and drug discovery
74. An evolutionary trace method defines binding surfaces common to protein families
75. Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
76. SCOP: A structural classification of proteins database
77. Genomics, gene expression and DNA arrays
78. Computational genetics: Finding protein function by nonhomology methods
79. Detecting protein function and protein-protein interactions from genome sequences
80. A combined algorithm for genome-wide prediction of protein function
81. A census of protein repeats
82. Comparative analysis of multiple protein-sequence alignment methods
83. Imagene: An integrated computer environment for sequence annotation and analysis
84. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%
85. JOY: Protein sequence-structure representation and analysis
86. Multiple DNA and protein sequence alignment based on segment-to-segment comparison
87. Benchmarking PSI-BLAST in genome annotation
88. A general method applicable to the search for similarities in the amino acid sequence of two proteins
89. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
90. Extracting protein alignment models from the sequence database
91. Highly specific protein sequence motifs for genome analysis
92. Extremophiles as a source of novel enzymes for industrial application
93. SAGA: Sequence alignment by genetic algorithm
94. T-Coffee: A novel method for fast and accurate multiple sequence alignment
95. Proteomics to study genes and genomes
96. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
97. A databank (3D-ali) collecting related protein sequences and structures
98. Improved tools for biological sequence comparison
99. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
100. Genome data shake tree of life
101. Multiple sequence alignment in phylogenetic analysis
102. Ballast: Blast post-processing based on locally conserved segments
103. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
104. An iterative method for faster sum-of-pairs multiple sequence alignment
105. Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments
106. Improved prediction of protein secondary structure by use of sequence profiles and neural networks
107. Protein secondary structure prediction using local alignments
108. Protein structure modelling for structural genomics
109. Minimal mutation trees of sequences
110. Large-scale comparison of protein sequence alignment algorithms with structure alignments
111. Finding function through structural genomics
112. A phylogenomic approach to microbial evolution
113. Phylogenetic inference in protein superfamilies: Analysis of SH2 domains
114. Structural genomics and its importance for gene function analysis
115. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling
116. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling
117. Identification of common molecular subsequences
118. Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies
119. Do more complex organisms have a greater proportion of membrane proteins in their genomes?
120. Multiple sequence alignment with the Divide-and-Conquer method
121. The COG database: A tool for genome-scale analysis of protein functions and evolution
122. Multiple sequence alignment by a pairwise algorithm
123. Multiple protein sequence alignment using double-dynamic programming
124. Advances in structural genomics
125. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
126. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
127. BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
128. A comprehensive comparison of multiple sequence alignment programs
129. DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
130. Seamless integration of biological applications within a database framework
131. Recent developments and future directions in computational genomics
132. Protein secondary structure prediction by the analysis of variation and conservation in multiple alignments
133. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
134. Secator: A program for inferring protein subfamilies from phylogenetic trees
135. A genetic algorithm for multiple molecular sequence alignment
136. In unison: Regularization of protein secondary structure predictions that makes use of multiple sequence alignments