Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set

Bioinformatics

Volumn 17, Issue 8, 2001, Pages 713-720

  Karplus, Kevin ^a   Hu, Birong ^a  

^a University of California Santa Cruz   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; CLINICAL PROTOCOL; CONTROLLED STUDY; DATA BASE; EVALUATION; INTERNET; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STANDARD;

EID: 0034855972     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.8.713     Document Type: Article

References (31)

1. Basic local alignment search tool
2. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
3. Amino acid substitution matrices from an information theoretic perspective
4. A model of evolutionary change in proteins
5. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
6. Multiple sequence alignment: Algorithms and applications
7. Analysis and prediction of functional sub-types from protein sequence alignments
8. Using CLUSTAL for multiple sequence alignments
9. Protein folds and families: Sequence and structure alignments
10. Hidden Markov models for sequence analysis: Extension and analysis of the basic method
11. Multiple sequence alignment with Clustal X
12. Hidden Markov models for detecting remote protein homologies
13. Predicting protein structure using only sequence information
14. Quantification of secondary structure prediction improvement using multiple alignments
15. Dialign: Finding local similarities by multiple sequence alignment
16. SAGA: Sequence alignment by genetic algorithm
17. A-Coffee: A novel method for fast and accurate multiple sequence alignment
18. Intermediate sequences increase the detection of homology between sequences
19. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
20. Easy method to predict solvent accessibility from multiple protein sequence alignments
21. Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology
22. Pattern-Induced Multi-sequence Alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling
23. Identification of common molecular subsequences
24. Reduced space hidden Markov model training
25. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice
26. BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
27. A comprehensive comparison of multiple sequence alignment programs