The UniMarker (UM) method for synteny mapping of large genomes.
BACKGROUND
Synteny mapping, or detecting regions that are orthologous between two genomes, is a key step in studies of comparative genomics. For completely sequenced genomes, this is increasingly accomplished by whole-genome sequence alignment. However, such methods are computationally expensive, especially for large genomes, and require rather complicated post-processing procedures to filter out non-orthologous sequence matches.


RESULTS
We have developed a novel method that does not require sequence alignment for synteny mapping of two large genomes, such as the human and mouse. In this method, the occurrence spectra of genome-wide unique 16mer sequences present in both the human and mouse genome are used to directly detect orthologous genomic segments. Being sequence alignment-free, the method is very fast and able to map the two mammalian genomes in one day of computing time on a single Pentium IV personal computer. The resulting human-mouse synteny map was shown to be in excellent agreement with those produced by the Mouse Genome Sequencing Consortium (MGSC) and by the Ensembl team; furthermore, the syntenic relationship of segments found only by our method was supported by BLASTZ sequence alignment.
Liao
Ben-Yang
BY
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
Chang
Yu-Jung
YJ
Ho
Jan-Ming
JM
Hwang
Ming-Jing
MJ
D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D002885:Chromosomes, Human, Pair 16 / Q000235:genetics*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D015894:Genome, Human; D044404:Genomic Islands / Q000235:genetics; D006801:Humans; D051379:Mice; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013045:Species Specificity; D014584:User-Computer Interface