Gene TRACE-reconstruction of gene content of ancestral species

Bioinformatics

Volumn 19, Issue 11, 2003, Pages 1412-1416

  Kunin, Victor ^a   Ouzounis, Christos A ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC ANALYSIS; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; PHYLOGENETIC TREE CONSTRUCTION METHOD; PRIORITY JOURNAL; PROTEIN FAMILY; SENSITIVITY AND SPECIFICITY; SPECIES; VALIDATION PROCESS; ALGORITHM; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; EVALUATION; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; GENOME; METHODOLOGY; PHYLOGENY; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL MODEL; VALIDATION STUDY;

ALGORITHMS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME; LINEAR MODELS; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; PROTEINS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; VARIATION (GENETICS);

EID: 0038589571     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg174     Document Type: Article

References (14)

1. Enright,A.J., Van Dongen,S. and Ouzounis,C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
2. Korbel,J.O., Snel,B., Huynen,M.A. and Bork,P. (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet., 18, 158-162.
3. Liberles,D.A., Thorén,A., von Heije,G. and Elofsson,A. (2002) The use of phylogenetic profiles for gene predictions. Curr. Genomics, 3, 131-137.
4. Maidak,B.L., Cole,J.R., Lilburn,T.G., Parker,C.T. and Jr.Saxman,P.R. et al. (2001) The RDP-II (Ribosomal Database Project. Nucleic Acids Res., 29, 173-174.
5. Marcotte,E.M., van Der Bliek,A.M. and Eisenberg,D. (2000) Localizing proteins in the cell from their phylogenetic profiles. Proc. Natl Acad. Sci. USA, 97, 12115-12120.
6. Mirkin,B.G., Fenner,T.I., Galperin,M.Y. and Koonin,E.V. (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol., 3.
7. Moran,N.A. (2002) Microbial minimalism: genome reduction in bacterial pathogens. Cell, 108, 583-586.
8. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
9. Pupko,T., Pe'er,I., Shamir,R. and Graur,D. (2000) A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol., 17, 890-896.
10. Snel,B., Bork,P. and Huynen,M.A. (1999) Genome phylogeny based on gene content. Nat. Genet., 21, 108-110.
11. Snel,B., Bork,P. and Huynen,M.A. (2002) Genomes in flux: the evolution of archaeal and protcobacterial gene content. Genome Res., 12, 17-25.
12. Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
13. Vert,J.-P. (2002) A tree kernel to analyse phylogenetic profiles. Bioinformatics, 18, S276-S284.
14. Wiens,J.J. and Servedio,M.R. (1999) Phylogenetic analysis and intraspecific variation: performance of parsimony, likelihood, and distance methods. Syst. Biol., 48, 228-253.