Comparative genome analysis

Methods of Biochemical Analysis

Volumn 43, Issue , 2001, Pages 359-392

  Galperin, Michael Y ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ANIMAL; ARTICLE; BACILLUS SUBTILIS; BIOLOGY; COMPARATIVE STUDY; ESCHERICHIA COLI; FACTUAL DATABASE; GENETICS; GENOME; GLYCOLYSIS; MYCOPLASMA; PHYLOGENY; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

ANIMALS; BACILLUS SUBTILIS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; ESCHERICHIA COLI; GENOME; GLYCOLYSIS; MYCOPLASMA; PHYLOGENY; PROTEINS; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

EID: 0035223823     PISSN: 00766941     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Review

References (41)

1. Andrade, M. A., Brown, N. P., Leroy, C., et al. (1999). Automated genome sequence analysis and annotation. Bioinformatics. 15, 391-412.
2. Bateman, A., Birney, E., Durbin, R., Eddy, S. R., Howe, K. L., and Sonnhammer, E. L. (2000). The pfam protein families database. Nucleic Acids Res. 28, 263-266.
3. Bhatia, U., Robison, K., and Gilbert, W. (1997). Dealing with database explosion: a cautionary note. Science. 276, 1724-1725.
4. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., et al. (1997). The complete genome sequence of Escherichia coli K-12. Science. 277, 1453-1474.
5. Bork, P., and Koonin, E. V. (1994). A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity. Proteins. 20, 347-355.
6. Brenner, S. E. (1999). Errors in genome annotation. Trends Genet. 15, 132-133.
7. Bult, C. J., White, O., Olsen, G. J., et al. (1996). Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 273, 1058-1073.
8. Corpet, F., Servant, F., Gouzy, J., and Kahn, D. (2000). ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28, 267-269.
9. Enright, A. J., Illopoulos, I., Kyrpides, N. C., and Ouzounis, C. A. (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature. 402, 86-90.
10. Fitch, W. M. (1970). Distinguishing homologous from analogous proteins. Syst. Zool. 19, 99-113.
11. Fleischmann, R. D., Adams, M. D., White, O., et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269, 496-512.
12. Fraser, C. M., Gocayne, J. D., White, O., et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science. 270, 397-403.
13. Frishman, D., and Mewes, H.-W. (1997). PEDANTic genome analysis. Trends Genet. 13, 415-416.
14. Gaasterland, T., and Ragan, M. A. (1998). Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb Comp Genomics. 3, 199-217.
15. Galperin, M. Y., Aravind, L., and Koonin, E. V. (2000). Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea. FEMS Microbiol. Lett. 183, 259-264.
16. Galperin, M. Y., Bairoch, A., and Koonin, E. V. (1998). A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases. Protein Sci. 7, 1829-1835.
17. Galperin, M. Y., and Koonin, E. V. (1998). Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. InSilico Biol. 1, 55-67.
18. Goffeau, A., Barrell, B. G., Bussey, H., et al. (1996). Life with 6000 genes. Science. 274, 546-567.
19. Henikoff, S., Greene, E. A., Pietrokovski, S., Bork, P., Attwood, T. K., and Hood, L. (1997). Gene families: the taxonomy of protein paralogs and chimeras. Science. 278, 609-614.
20. Hoersch, I., Leroy, I., Brown, N. P., Andrade, M. A., and Sander, I. (2000). The GeneQuiz web server: protein functional analysis through the Web. Trends Biochem Sci. 25, 33-35.
21. Huynen, M. A., Diaz-Lazcoz, Y., and Bork, P. (1997). Differential genome display. Trends Genet. 13, 389-390.
22. Huynen, M. A., and Snel, B. (2000). Gene and context: integrative approaches to genome analysis. Adv. Protein Chem. 54, 345-379.
23. Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30.
24. Koonin, E. V. (1997). Genome sequences: genome sequence of a model prokaryote. Curr. Biol. 7, R656-R659.
25. Koonin, E. V., Mushegian, A. R., Galperin, M. Y., and Walker, D. R. (1997). Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25, 619-637.
26. Kunst, F., Ogasawara, N., Moszer, I., et al. (1997). The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 390, 249-256.
27. Marcotte, E. M., Pellegrini, M., Ng, H. L., Rice, D. W., Yeates, T. O., and Eisenberg, D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science. 285, 751-753.
28. Medigue, C., Rechenmann, F., Danchin, A., and Viari, A. (1999). Imagene: an integrated computer environment for sequence annotation and analysis. Bioinformatics. 15, 2-15.
29. Natale, D. A., Galperin, M. Y., Tatusov, R. L., and Koonin, E. V. (2000). Using the COG database to improve gene recognition in complete genomes. Genetica. 108, 9-17.
30. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D., and Maltsev, N. (1999). The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. U. S.A. 96, 2896-2901.
31. Overbeek, R., Larsen, N., Pusch, G. D., D'Souza, M., Jr, E. S., Kyrpides, N., Fonstein, M., Maltsev, N., and Selkov, E. (2000). WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28, 123-125.
32. 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. U.S.A. 96, 4285-4288.
33. Schultz, J., Copley, R. R., Doerks, T., Ponting, C. P. and Bork, P. (2000). SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28, 231-234.
34. Schultz, J., Milpetz, F., Bork, P. and Ponting, C. P. (1998). SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. U.S.A. 95, 5857-5864.
35. Snel, B., Bork, P., and Huynen, M. (2000). Genome evolution. Gene fusion versus gene fission. Trends Genet. 16, 9-11.
36. Tatusov, R. L., Galperin, M. Y., Natale, D. A., and Koonin, E. V. (2000). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36.
37. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997). A genomic perspective on protein families. Science. 278, 631-637.
38. Taylor, B. L. and Zhulin, I. B. (1999). PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63, 479-506.
39. Tuininga, J. E., Verhees, C. H., van der Oost, J., Kengen, S. W., Stams, A. J., and de Vos, W. M. (1999). Molecular and biochemical characterization of the ADP-dependent phosphofructokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 274, 21023-21028.
40. Walker, D. R., and Koonin, E. V. (1997). SEALS: a system for easy analysis of lots of sequences. ISMB. 5, 333-339.
41. Wootton, J. C., and Federhen, S. (1996). Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266, 554-71.