Fast identification and statistical evaluation of segmental homologies in comparative maps

Bioinformatics

Volumn 19, Issue SUPPL. 1, 2003, Pages

  Calabrese, Peter P ^a   Chakravarty, Sugata ^b   Vision, Todd J ^c  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b University of North Carolina at Chapel Hill   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Comparative maps; Genome evolution; Homology; Synteny

Indexed keywords

ALGORITHM; BIOINFORMATICS; CHROMOSOME MAP; COMPUTER PROGRAM; CONFERENCE PAPER; GENE DUPLICATION; GENE IDENTIFICATION; GENE MAPPING; GENOME ANALYSIS; PRIORITY JOURNAL; SEGMENTAL HOMOLOGY; SEQUENCE HOMOLOGY; SPECIES DIVERSITY; STATISTICAL ANALYSIS; STRUCTURAL HOMOLOGY; SYNTENY; ARABIDOPSIS; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; GENOME; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; STATISTICAL MODEL; VALIDATION STUDY;

ALGORITHMS; ARABIDOPSIS; BASE SEQUENCE; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; VARIATION (GENETICS);

EID: 1042276327     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg1008     Document Type: Conference Paper

References (19)

1. Arratia, R., Goldstein, L. and Gordon, L. (1990) Poisson approximation and the Chen-Stein method. Statistical Science, 5, 403-424.
2. Delcher, A.L., Kasif, S., Fleischmann, R.D., Peterson, J., White, O. and Salzberg, S.L. (1999) Alignment of whole genomes. Nucleic Acids Res., 27, 2369-2376.
3. Durand, D. and Sankoff, D. (2002) Tests for gene clustering. RECOMB 2002, 144-154.
4. Fujibuchi, W., Ogata, H., Matsuda, H. and Kanehisa, M. (2000) Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res., 28, 4029-4036.
5. Gaut, B.S. (2001) Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res., 11, 55-66.
6. Goldberg, D.S., McCouch, S. and Kleinberg, J. (2000) Algorithms for constructing comparative maps. In Sankoff, D. and Nadeau, J.H. (eds), Comparative Genomics. Kluwer, Dordrecht, pp. 243-261.
7. Hall, P. (1988) Introduction to the Theory of Coverage Processes. Wiley, New York.
8. Huynen, M.A., Snel, B. and Bork, P. (2001) Inversions and the dynamics of eukaryotic gene order. Trends Genet., 17, 304-306.
9. Kihara, D. and Kanehisa, M. (2000) Tandem clusters of membrane proteins in complete genome sequences. Genome Res., 10, 731-743.
10. Ku, H.-M., Vision, T.J., Liu, J. and Tanksley, S.D. (2000) Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl Acad. Sci. USA, 97, 9121-9126.
11. Lynch, M. and Conery, J. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
12. Sedgewick, R. (1990) Algorithms in C. Addison-Wesley, Reading, MA, pp. 479-481.
13. Seoighe, C., Federspiel, N., Jones, T., Hansen, N., Bivolarovic, V., Surzycki, R., Tamse, R., Komp, C., Huizar, L., Davis, R.W. et al. (2000) Prevalence of small inversions in yeast gene order evolution. Proc. Natl Acad. Sci. USA, 97, 14433-14437.
14. Simillion, C., Vandepoele, K., Van Montagu, M.C., Zabeau, M. and Van De Peer, Y. (2002) The hidden duplication past of Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 99, 13627-13632.
15. Sonnhammer, E.L. and Durbin, R. (1997) Analysis of protein domain families in C.elegans. Genomics, 46, 200-216.
16. Vandepoele, K., Saeys, Y., Simillion, C., Raes, J. and Van De Peer, Y. (2002) The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res., 12, 1792-1801.
17. Vision, T.J., Brown, D.G. and Tanksley, S.D. (2000) The origins of genomic duplications in Arabidopsis. Science, 290, 2114-2117.
18. Vision, T.J. and Brown, D.G. (2000) Genome archaeology: detecting ancient polyploidy in contemporary genomes. In Sankoff, D. and Nadeau, J.H. (eds), Comparative Genomics. Kluwer, Dordrecht, pp. 479-492.
19. Wolfe, K.H. (2001) Yesterday's polyploids and the mystery of diploidization. Nature Genetics Reviews, 2, 333-341.