DRIMM-Synteny: decomposing genomes into evolutionary conserved segments.
BACKGROUND
The rapidly increasing set of sequenced genomes highlights the importance of identifying the synteny blocks in multiple and/or highly duplicated genomes. Most synteny block reconstruction algorithms use genes shared over all genomes to construct the synteny blocks for multiple genomes. However, the number of genes shared among all genomes quickly decreases with the increase in the number of genomes.


RESULTS
We propose the Duplications and Rearrangements In Multiple Mammals (DRIMM)-Synteny algorithm to address this bottleneck and apply it to analyzing genomic architectures of yeast, plant and mammalian genomes. We further combine synteny block generation with rearrangement analysis to reconstruct the ancestral preduplicated yeast genome.


BACKGROUND
kspham@cs.ucsd.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Pham
Son K
SK
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA. kspham@cs.ucsd.edu
Pevzner
Pavel A
PA
D000465:Algorithms; D000818:Animals; D017124:Conserved Sequence / Q000235:genetics*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D008322:Mammals; D012984:Software; D026801:Synteny