« Previous
Next »
Artificial Intelligence in Medicine
Volume 35, Issue 1
, Pages 9-18
, September 2005
Finding the biologically optimal alignment of multiple sequences
References
- . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970;48:443–453
- . Near optimal multiple alignment within a band in polynomial time. In: Yao F, Luks E editor. Proceedings of the 32nd annual ACM symposium on theory of computing (STOC 2000). New York: ACM Press; 2000;p. 425–34
- . Strategies for multiple sequence alignment. Biotechniques. 2002;32:572–574
- . Recent progress in multiple sequence alignement. Pharmacogenomics. 2002;3:131–144
- . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res. 1994;22(22):4673–4680
- . Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University Press; 1998;
- . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res. 2004;32:1792–1794
- The pfam protein families database. Nucl Acids Res. 2004;32:D138–D141
- Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Bioinformatics. 1995;12:327–345
- . Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images. IEEE Trans Pattern Anal Mach Intell. 1984;6(6):721–742
- . Markov chain Monte Carlo: stochastic simulation for Bayesian inference. Chapman & Hall; 1997;
- . Markov chain Monte Carlo in practice: a roundtable discussion. Am Statistician. 1998;52:93–100
- . Multiple alignment using hidden Markov models. In: Clark D, Altman R, Hunter L, Lengauer T, Wodak S, Rawlings C editor. Proceedings of the third international conference on intelligent systems for molecular biology (ISMB-95). Menlo Park, CA: AAAI Press; 1995;p. 114–20
- . Gibbs recursive sampler: finding transcription factor binding sites. Nucl Acids Res. 2003;31:3580–3585
- . Deterministic annealing for clustering, compression, classification, regression, and related optimization problems. Proc IEEE. 1998;86:2210–2239
- . Maximum likelihood from incomplete data via the EM algorithm (with discussion). J R Statistical Soc. 1977;39:1–38Series B
- . Exhaustive enumeration of protein domain families. J Mol Biol. 2003;328:749–767
- . Statistical methods in bioinformatics. New York: Springer-Verlag; 2001;
- . A model of evolutionary change in proteins. In: Dayhoff MO editors. Atlas of protein sequence and structure, vol. 5. Washington: National Biomedical Research Foundation; 1978;p. 345–52
- . Deterministic annealing EM algorithm. Neural Networks. 1998;11:271–282
PII: S0933-3657(05)00062-X
doi: 10.1016/j.artmed.2005.01.007
© 2005 Elsevier B.V. All rights reserved.
« Previous
Next »
Artificial Intelligence in Medicine
Volume 35, Issue 1
, Pages 9-18
, September 2005
