PanOCT: Automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species

Nucleic Acids Research

Volumn 40, Issue 22, 2012, Pages

  Fouts, Derrick E ^a   Brinkac, Lauren ^a   Beck, Erin ^a   Inman, Jason ^a   Sutton, Granger ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; AUTOMATION; BACTERIAL GENOME; BACTERIAL STRAIN; COMPUTER PROGRAM; GENE CLUSTER; GENE ORDER; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CONSERVATION; INTERMETHOD COMPARISON; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PARALOGY; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

BACTERIA; BACTERIAL PROTEINS; CLUSTER ANALYSIS; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; SOFTWARE;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84871199596     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks757     Document Type: Article

References (26)

1. Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S. et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc. Natl Acad. Sci. USA, 102, 13950-13955.
2. Tettelin, H., Riley, D., Cattuto, C. and Medini, D. (2008) Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol., 11, 472-477.
3. Fitch, W. M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
4. Kuzniar, A., van Ham, R. C., Pongor, S. and Leunissen, J. A. (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends Genet., 24, 539-551.
5. Kristensen, D. M., Wolf, Y. I., Mushegian, A. R. and Koonin, E. V. (2011) Computational methods for Gene Orthology inference. Brief. Bioinform., 12, 379-391.
6. Gabaldon, T. (2008) Large-scale assignment of orthology: back to phylogenetics? Genome. Biol., 9, 235.
7. Huynen, M. A. and Bork, P. (1998) Measuring genome evolution. Proc. Natl Acad. Sci. USA, 95, 5849-5856.
8. Remm, M., Storm, C. E. and Sonnhammer, E. L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314, 1041-1052.
9. Li, L., Stoeckert, C. J. Jr and Roos, D. S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome. Res., 13, 2178-2189.
10. Crabtree, J., Angiuoli, S. V., Wortman, J. R. and White, O. R. (2007) In: Ochs, M. F. (ed. ), Gene Function Analysis. Humana Press Inc, Totowa, NY, pp. 93-108.
11. Zhang, A., Yang, M., Hu, P., Wu, J., Chen, B., Hua, Y., Yu, J., Chen, H., Xiao, J. and Jin, M. (2011) Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC Genomics, 12, 523.
12. Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C. L., Dalin, E., Tu, H., Huang, E., Barry, K. et al. (2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol., 12, R20.
13. Mazzaglia, A., Studholme, D. J., Taratufolo, M. C., Cai, R., Almeida, N. F., Goodman, T., Guttman, D. S., Vinatzer, B. A. and Balestra, G. M. (2012) Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of Kiwifruit outbreaks belong to the same genetic lineage. PLoS One, 7, e36518.
14. Biggs, P. J., Fearnhead, P., Hotter, G., Mohan, V., Collins-Emerson, J., Kwan, E., Besser, T. E., Cookson, A., Carter, P. E. and French, N. P. (2011) Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS One, 6, e27121.
15. Krauland, M. G., Dunning Hotopp, J. C., Riley, D. R., Daugherty, S. C., Marsh, J. W., Messonnier, N. E., Mayer, L. W., Tettelin, H. and Harrison, L. H. (2012) Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States. PLoS One, 7, e35699.
16. Bidossi, A., Mulas, L., Decorosi, F., Colomba, L., Ricci, S., Pozzi, G., Deutscher, J., Viti, C. and Oggioni, M. R. (2012) A functional genomics approach to establish the complement of carbohydrate transporters in Streptococcus pneumoniae. PLoS One, 7, e33320.
17. Haft, D. H., Selengut, J. D. and White, O. (2003) The TIGRFAMs database of protein families. Nucleic Acids Res, 31, 371-373.
18. Denielou, Y. P., Sagot, M. F., Boyer, F. and Viari, A. (2011) Bacterial syntenies: an exact approach with gene quorum. BMC Bioinformatics, 12, 193.
19. Novichkov, P. S., Ratnere, I., Wolf, Y. I., Koonin, E. V. and Dubchak, I. (2009) ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res., 37, D448-D454.
20. Byrne, K. P. and Wolfe, K. H. (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res., 15, 1456-1461.
21. Seret, M. L. and Baret, P. V. (2011) IONS: Identification of orthologs by neighborhood and similarity-an automated method to identify orthologs in chromosomal regions of common evolutionary ancestry and its application to hemiascomycetous yeasts. Evol. Bioinform. Online, 7, 123-133.
22. 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.
23. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
24. Davidsen, T., Beck, E., Ganapathy, A., Montgomery, R., Zafar, N., Yang, Q., Madupu, R., Goetz, P., Galinsky, K., White, O. et al. (2010) The comprehensive microbial resource. Nucleic Acids Res., 38, D340-D345.
25. Madupu, R., Brinkac, L. M., Harrow, J., Wilming, L. G., Bohme, U., Lamesch, P. and Hannick, L. I. (2010) Meeting report: a workshop on Best Practices in Genome Annotation. Database, 2010, baq001.
26. Purushe, J., Fouts, D. E., Morrison, M., White, B. A., Mackie, R. I., Coutinho, P. M., Henrissat, B. and Nelson, K. E. (2010) Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb. Ecol., 60, 721-729.