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The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

Klaas Vandepoele (UGent) , Yvan Saeys (UGent) , Cedric Simillion (UGent) , Jeroen Raes (UGent) and Yves Van de Peer (UGent)
(2002) GENOME RESEARCH. 12(11). p.1792-1801
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Abstract
It is expected that one of the merits of comparative genomics lies in the transfer of structural and functional information from one genome to another. This is based on the observation that, although the number of chromosomal rearrangements that occur in genomes is extensive, different species still exhibit a certain degree of conservation regarding gene content and gene order. It is in this respect that we have developed a new software tool for the Automatic Detection of Homologous Regions (ADHoRe). ADHoRe was primarily developed to find large regions of microcolinearity, taking into account different types of microrearrangements such as tandem duplications, gene loss and translocations, and inversions. Such rearrangements often complicate the detection of colinearity, in particular when comparing more anciently diverged species. Application of ADHoRe to the complete genome of Arabidopsis and a large collection of concatenated rice BACs yields more than 20 regions showing statistically significant microcolinearity between both plant species. These regions comprise from 4 up to 11 conserved homologous gene pairs. We predict the number of homologous regions and the extent of microcolinearity to increase significantly once better annotations of the rice genome become available.
Keywords
GENOME EVOLUTION, COMPARATIVE SEQUENCE-ANALYSIS, GRASS GENOMES, COMPARATIVE GENETICS, THALIANA, COLINEARITY, ANNOTATION, SEGMENTS, SYNTENY, MAIZE

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Chicago
Vandepoele, Klaas, Yvan Saeys, Cedric Simillion, Jeroen Raes, and Yves Van de Peer. 2002. “The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice.” Genome Research 12 (11): 1792–1801.
APA
Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., & Van de Peer, Y. (2002). The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. GENOME RESEARCH, 12(11), 1792–1801.
Vancouver
1.
Vandepoele K, Saeys Y, Simillion C, Raes J, Van de Peer Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. GENOME RESEARCH. 2002;12(11):1792–801.
MLA
Vandepoele, Klaas, Yvan Saeys, Cedric Simillion, et al. “The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice.” GENOME RESEARCH 12.11 (2002): 1792–1801. Print.
@article{154141,
  abstract     = {It is expected that one of the merits of comparative genomics lies in the transfer of structural and functional information from one genome to another. This is based on the observation that, although the number of chromosomal rearrangements that occur in genomes is extensive, different species still exhibit a certain degree of conservation regarding gene content and gene order. It is in this respect that we have developed a new software tool for the Automatic Detection of Homologous Regions (ADHoRe). ADHoRe was primarily developed to find large regions of microcolinearity, taking into account different types of microrearrangements such as tandem duplications, gene loss and translocations, and inversions. Such rearrangements often complicate the detection of colinearity, in particular when comparing more anciently diverged species. Application of ADHoRe to the complete genome of Arabidopsis and a large collection of concatenated rice BACs yields more than 20 regions showing statistically significant microcolinearity between both plant species. These regions comprise from 4 up to 11 conserved homologous gene pairs. We predict the number of homologous regions and the extent of microcolinearity to increase significantly once better annotations of the rice genome become available.},
  author       = {Vandepoele, Klaas and Saeys, Yvan and Simillion, Cedric and Raes, Jeroen and Van de Peer, Yves},
  issn         = {1088-9051},
  journal      = {GENOME RESEARCH},
  language     = {eng},
  number       = {11},
  pages        = {1792--1801},
  title        = {The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice},
  url          = {http://dx.doi.org/10.1101/gr.400202},
  volume       = {12},
  year         = {2002},
}

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