Greedy method for inferring tandem duplication history

Bioinformatics

Volumn 19, Issue 12, 2003, Pages 1497-1504

  Zhang, Louxin ^a   Ma, Bin ^b   Wang, Lusheng ^c   Xu, Ying ^d  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b UNIVERSITY OF WESTERN ONTARIO   (Canada)

^c CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^d PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MUCIN; ZINC FINGER PROTEIN;

ALGORITHM; ARTICLE; GENE DUPLICATION; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; OLFACTORY RECEPTOR; PHYLOGENY; PRIORITY JOURNAL; SIMULATION; TANDEM REPEAT; VALIDATION PROCESS;

EID: 0041886965     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg191     Document Type: Article

References (19)

1. Benson,G. and Dong,L. (1999) Reconstructing the duplication history of a tandem repeat. In Proceedings of ISMB'99. pp. 44-53.
2. Dehal,P. et al. (2001) Human chromosome 19 and related regions in mouse: Conservative and lineage-specific evolution. Science, 293, 104-111.
3. Desseyn,J.L. et al. (1997) Human mucin gene MUC5B, the 10.7kb large central exon encodes various alternate subdomains resulting in a super-repeat. Structural evidence for a 11p15.5 gene family. J. Bio. Chem., 272, 3168-3178.
4. Desseyn,J.L. et al. (2000) Evolution of the large secreted gel-forming mucins. Mol. Biol. Evol., 17, 1175-1184.
5. Elemento,O., Gascuel,O. and Lefranc,M.-P. (2002) Reconstructing the duplication history of tandemly repeated genes. Mol. Biol. Evol., 19, 278-288.
6. Fitch,W. (1977) Phylogenies constrained by cross-over process as illustrated by human hemoglobins in a thirteen cycle, eleven amino-acid repeat in human apolipoprotein A-I. Genetics, 86, 623-644.
7. Felsentein,J. (1995) PHYLIP, version 3.57c. Department of Genetics, University of Washington, Seattle.
8. Huang,X. (1994) On global sequence alignment. Comput. Appl. Biosci., 10, 227-235.
9. Jaitly,D. et al. (2001) Methods for reconstructing the history of tandem repeats and their application to the human genome. J. Comp.. Sci. Sys., in press.
10. Kim,J. et al. (2001) Homology-driven assembly of a sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene-rich euchromatic segments of human chromosome 19. Genomics, 74, 129-141.
11. Kuhner,M.K. and Felsenstein,J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol., 11, 459-468. (Erratum 12: 525 1995).
12. Li,M., Tromp,J. and Zhang,L. (1996) On the nearest neighbor interchange distance between evolutionary trees. J. Theor. Biol., 182, 463-467.
13. Lim,A. and Zhang,L. (1999) WebPHYLIP: a web-interface to PHYLIP. Bioinformatics, 12, 1068-1069.
14. Ohno,S. (1970) Evolution by Gene Duplication. Springer, New York.
15. Pigny,P., et al. (1996) Human mucin genes assigned to 11P15.5: identification and organization of a cluster of genes. Genomics, 8, 340-352.
16. Shen,S., Slightom,J. and Smithies,O. (1981) A history of the human fetal globin gene duplication. Cell, 26, 191-203.
17. Rambaut,A. and Grassly,N.C. (1997) Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13, 235-238.
18. Swofford,D.L. et al. (1996) Phylogeny inference. In Hillis,D.M. et al., (eds), Molecular Systematic. Sinauer Associate, MA, pp. 407-514.
19. Tang,M., Waterman,M. and Yooseph,S. (2001) Zinc finger gene clusters and tandem gene duplication. In Proceedings of RECOMB'01. pp. 297-304.