Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree

Journal of Molecular Evolution

Volumn 44, Issue 2, 1997, Pages 226-233

  Dopazo, Joaquín ^a   Carazo, José María ^b  

^a TDI   (Spain)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

Classification; Neural network; Phylogeny; Self organization

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER SIMULATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; TAXONOMY;

ALGORITHMS; COMPUTER SIMULATION; HUMANS; NEURAL NETWORKS (COMPUTER); NUCLEIC ACIDS; PHYLOGENY; PROTEINS; RIBOSOMAL PROTEINS; RNA-BINDING PROTEINS;

EID: 0031042985     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006139     Document Type: Article

References (38)

1. Adell JC, Dopazo J (1994) Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates. J Mol Evol 38:305-309
2. Andrade MA, Casari G, Sander C, Valencia A (1996) Classification of protein families and detection of the determinant residues with a self-organising neural network. (submitted).
3. Arrigo P, Guiuliano F, Scalia F, Rapallo A, Damiani G (1991) Identification of a new motif on nucleic acid sequence data using Kohonen's self-organizing map. Comput Appl Biosci 7:353-357
4. Bengio Y, Pouliot Y (1990) Efficient recognition of immunological domains from amino acid sequences using a neural network. Comput Appl Biosci 6:319-324
5. Bohr H, Bohr J, Brunak S, Cotterill R, Lautrup B, Norskov L, Olsen OH, Petersen SB (1988) Protein secondary structure and homology by neural networks. The a helices in rhodopsin. FEBS Lett 241: 223-228
6. Casari G, Sander C, Valencia A (1995) Functional residues predicted in protein sequence space. Nat Struct Biol 2:171-178
7. Clark AG, Lanigan CMS (1993) Prospects for estimating nucleotide divergence with RAPDs. Mol Biol Evol 10:1096-1111
8. Dopazo J (1994) Estimating errors and confidence intervals for branch lengths in phylogenetic trees by a bootstrap approach. J Mol Evol 38:300-304
9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
10. Felsenstein J (1993) PHYLIP (phylogeny inference package) version 3.5. Department of Genetics, University of Washington, Seattle
11. Ferran EA, Ferrara P (1991) Topological maps of protein sequences. Biol Cybern 65:451-458
12. Ferran EA, Ferrara P (1992) Clustering proteins into families using artificial neural networks. Comput Appl Biosci 8:39-44
13. Ferran EA, Pflugfelder B (1993) A hybrid method to cluster protein sequences based on statistic and artificial neural networks. Comput Appl Biosci 9:671-680
14. Ferran EA, Pflugfelder B, Ferrara P (1994) Self-organized neural maps of human protein sequences. Protein Sci 3:507-521
15. Fitch, WM (1971) Toward defining the course of evolution: minimum change for a specified tree topology. Syst Zool 20:406-416
16. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279-284
17. Frishman D, Argos P (1992) Recognition of distantly related protein sequences using conserved motifs and neural networks. J Mol Biol 228:951-962
18. Fritzke B (1994) Growing cell structures - a self-organizing network for unsupervised and supervised learning. Neural Networks 7: 1141-1160
19. Henikoff S, Henikoff JG (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res 19:6565-6572
20. Hirst JD, Stenberg MJE (1992) Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochemistry 32:7211-7218
21. Holmes EC, Garnett GP (1994) Genes, trees and infections: molecular evidence in epidemiology. Trends Ecol Evol 9:256-260
22. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York pp 21-132
23. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
24. Kohonen T (1990) The self-organizing map. Proc IEEE 78:1464-1480
25. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
26. Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269-5273
27. O'Neill MC (1995) Escherichia coli promoters: neural networks develop distinct descriptors in learning to search for promoters of different spacing classes. Nucleic Acids Res 20:3471-3477
28. Petersen SB, Bohr H, Bohr J, Brunak S, Cotterill R, Fredholm H, Lautrup B (1990) Training neural networks to analyse biological sequences. Trends Biotechnol 8:304-308
29. Rost B, Sander C (1993a) Secondary structure prediction of all-helical proteins in two states. Protein Eng 6:831-836
30. Rost B, Sander C (1993b) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci USA 90:7558-7562
31. Saitou N, Imanishi T (1989) Relative efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol 6: 514-525
32. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
33. Snyder EE, Stormo GD (1995) Identification of protein coding regions in genomic DNA. J Mol Biol 248:1-18
34. Tateno Y, Nei M, Tajima F (1982) Accuracy of estimated phylogenetic trees for molecular data. I. Distantly related species. J Mol Evol 18:387-404
35. Wade RC, Bohr H, Wolynes PG (1992) Prediction of water binding sites on proteins by neural networks. J Am Chem Soc 114:8284-8285
36. Werbos PJ (1990) Backpropagation through time: what it does and how to do it. Proc IEEE 78:1550-1560
37. Wu C (1993) Classification neural networks for rapid sequence annotation and automated database organization. Comput Chem 17: 219-227
38. Wu C, Shivakumar S (1994) Back-propagation and counter-propagation neural networks for phylogenetic classification of ribosomal RNA sequences. Nucleic Acids Res 22:4291-4299