RT Journal
A1 Vandepoele, Klaas
A1 Saeys, Yvan
A1 Simillion, Cedric
A1 Raes, Jeroen
A1 Van de Peer, Yves
T1 The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice
JF Genome Research 
JO Genome Research 
YR 2002 
FD November 01 
VO 12 
IS 11 
SP 1792 
OP 1801 
DO 10.1101/gr.400202 
UL http://genome.cshlp.org/content/12/11/1792.abstract 
AB 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.