Inference of gene function based on gene fusion events: The rosetta-stone method

Methods in Molecular Biology

Volumn 396, Issue , 2007, Pages 31-41

  Suhre, Karsten ^a  

^a NONE

Author keywords

Functional networks; Gene fusion; Metabolic pathways; Nonhomology based function prediction; Protein complexes; Protein protein interaction; Rosetta stone method

Indexed keywords

PROTEIN;

ARTICLE; DIMERIZATION; GENE FUSION; GENETICS; METABOLISM; PHYLOGENY;

DIMERIZATION; GENE FUSION; PHYLOGENY; PROTEINS;

EID: 36549015556     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-515-6:31     Document Type: Article

References (19)

1. Galperin, M. Y. and Koonin, E. V. (2000) Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18, 609-613.
2. Sali, A. (1999) Functional links between proteins. Nature 402, 23-26.
3. Enright, A. J. and Ouzounis, C. A. (2001) Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol. 2, RESEARCH0034.
4. Marcotte, E. M. (2000) Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10, 359-365.
5. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O., and Eisenberg, D. (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402, 83-86.
6. von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., and Snel, B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258-261.
7. Mellor, J. C., Yanai, I., Clodfelter, K. H., Mintseris, J., and DeLisi, C. (2002) Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 30, 306-309.
8. Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
9. Suhre, K. and Claverie, J. M. (2004) FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res. 32, D273-D276.
10. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) A genomic perspective on protein families. Science 278, 631-637.
11. Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28.
12. Enault, F., Suhre, K., Abergel, C., Poirot, O., and Claverie, J. M. (2003) Annotation of bacterial genomes using improved phylogenomic profiles. Bioinformatics 19, i105-i107.
13. Enault, F., Suhre, K., Poirot, O., Abergel, C., and Claverie, J. M. (2003) Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes. Nucleic Acids Res. 31, 3720-3722.
14. Enault, F., Suhre, K., Poirot, O., Abergel, C., and Claverie, J. M. (2004) Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. Nucleic Acids Res. 32, W336-W339.
15. Pruitt, K. D., Tatusova, T., and Maglott, D. R. (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33, D501-D504.
16. Berman, H. M., Westbrook, J., Feng, Z., et al. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
17. Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217.
18. Poirot, O., Suhre, K., Abergel, C., O'Toole, E., and Notredame, C. (2004) 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. 32, W37-W40.
19. Felsenstein, J. (1989) PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166.