Towards a reliable objective function for multiple sequence alignments

Journal of Molecular Biology

Volumn 314, Issue 4, 2001, Pages 937-951

  Thompson, Julie D ^a   Plewniak, Frédéric ^a   Ripp, Raymond ^a   Thierry, Jean Claude ^a   Poch, Olivier ^a  

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

Author keywords

Alignment quality analysis; Bioinformatics; Genome analysis; Objective function; Sequence alignment

Indexed keywords

ENZYME; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; DATA BASE; GENOME ANALYSIS; MOLECULAR BIOLOGY; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

VIBRIO; VIBRIO CHOLERAE;

EID: 0035824873     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5187     Document Type: Article

References (47)

1. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
2. Hidden Markov models for detecting remote protein homologies
3. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
4. SAGA: Sequence alignment by genetic algorithm
5. Segment-based scores for pairwise and multiple sequence alignments
6. T-Coffee: A novel method for fast and accurate multiple sequence alignment
7. DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
8. Automated genome sequence analysis and annotation
9. The GeneQuiz web server: Protein functional analysis through the Web
10. Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture
11. Alfresco-A workbench for comparative genomic sequence analysis
12. Imagene: An integrated computer environment for sequence annotation and analysis
13. BaliBASE (Benchmark alignment dataBASE): Enhancements for repeats, transmembrane sequences and circular permutations
14. A comprehensive comparison of multiple sequence alignment programs
15. An iterative method for faster sum-of-pairs multiple sequence alignment
16. The multiple sequence alignment problem in biology
17. Darwin v. 2.0: An interpreted computer language for the biosciences
18. Evaluation measures of multiple sequence alignments
19. COFFEE: An objective function for multiple sequence alignments
20. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
21. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
22. Weighting in sequence space: A comparison of methods in terms of generalized sequences
23. InterPro - An integrated documentation resource for protein families, domains and functional sites
24. A model of evolutionary change in proteins
25. Performance evaluation of amino acid substitution matrices
26. Amino acid substitution during functionally constrained divergent evolution of protein sequences
27. Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
28. SCOP: A structural classification of proteins database
29. Twilight zone of protein sequence alignments
30. Statistical significance of protein structure prediction by threading
31. Accurate formula for P-values of gapped local sequence and profile alignments
32. A new approach to sequence comparison: Normalized sequence alignment
33. A measure of the similarity of sets of sequences not requiring sequence alignment
34. A sequence property approach to searching protein databases
35. Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment
36. Rapid similarity searches of nucleic acid and protein data banks
37. Gene descent, duplication and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases
38. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
39. Basic local alignment search tool
40. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
41. Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules
42. Twilight zone of protein sequence alignments
43. Multiple alignment of complete sequences (MACS) in the post-genomic era
44. Optimal sequence alignment using affine gap costs
45. An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited
46. The neighbor-joining method: A new method for reconstructing phylogenetic trees
47. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice